title: FAK transfected rat soleus muscle 425, unloaded + 5 days reloaded


title: empty transfected rat soleus muscle 426, unloaded + 5 days reloaded

status: Public on Dec 31 2009

type: RNA

city: Berne 9

first: Martin

last: Flück

state: Bern

address: Bühlstrase 26

department: Department of Anatomy

country: Switzerland

institute: University of Berne

description: CMV-driven empty expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 2 days after transfection, the soleus muscles were unloaded for 7 days by hindlimb suspension. Subsequent reloading was provoked by allowing the animals to return to normal cage activity for 5 days. The muscle was isolated, snap frozen and total RNA extracted

hyb_protocol: ATLAS ARRAY-BD Clontech 16h at 68degC in ExpressHyb, Washing: 4x in (2xSSC, 1% SDS) at68degC for 1h. 1x in (0.1xSSC, 0.5% SDS) at68degC for ? h, 1x in (2x SSC) atroom temperature for 5min

scan_protocol: Phosphoimager screen, 4-10 days

data_processing: raw data

label: reverse transcription of 3 microgram total RNA with gene specific primers at 50degC using Superscript II RT (Invitrogen)

molecule: total RNA

organism: Rattus norvegicus

source_name: Martin Flueck, Institute of Anatomy, University of Berne

label_protocol: alpha-32P]dATP, and modified dCTP (Ambion (Europe)

extract_protocol: Modified RNeasy mini kit (Qiagen)

tag: tissue

value: soleus muscle

tag: age

value: 3 month

tag: gender

value: female

tag: strain

value: Wistar


title: empty transfected rat soleus muscle 433, unloaded + one day reloaded

description: CMV-driven empty expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 2 days after transfection, the soleus muscles were unloaded for 7 days by hindlimb suspension. Subsequent reloading was provoked by allowing the animals to return to normal cage activity for 1 day. The muscle was isolated, snap frozen and total RNA extracted


title: HF-17267 16459_Xba

status: Public on Feb 18 2010

type: genomic

city: South San Francisco

first: Peter

last: Haverty

state: CA

address: 1 DNA Way

department: Bioinformatics

country: USA

institute: Genentech, Inc.

description:
Dissociation protocol: Mechanical
Enrichment protocol: FACS

hyb_protocol: Affymetrix 100K protocol

scan_protocol: Affymetrix 100K protocol

data_processing: Affymetrix 100K Mapping Array intensity signal CEL files were processed by dChip 2005 (Build date Nov 30, 2005) using the PM/MM difference model and invariant set normalization.  Ninety normal samples were downloaded from the Affymetrix website (http://www.affymetrix.com/support/technical/byproduct.affx?product=100k) and analyzed at the same time.  One CEL file for each set (Xba and Hind) with the median signal intensity across the set was selected as the reference array.   The dChip-normalized signal intensities were converted to log2 ratios and segmented as follows.  For each autosomal probe set, the log2 tumor/normal ratio of each tumor sample was calculated using the average intensity for each probe set in the normal set.  The log2 ratios were centered to a median of zero and segmented using the GLAD package for the R statistical environment.

label: biotin

molecule: genomic DNA

organism: Homo sapiens

source_name: Pancreatic Adenocarcinoma Tissue

label_protocol: Affymetrix 100K protocol

extract_protocol: Qiagen DNA extraction kit was used according to the manufacturer's instructions

tag: Nonsorted


title: HF-17203 16455_Xba


title: empty transfected rat soleus muscle 432, unloaded + one day reloaded


title: empty transfected rat soleus muscle 431, unloaded + one day reloaded


title: FAK transfected rat soleus muscle 431, unloaded + one day reloaded

description: CMV-driven FAK expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 2 days after transfection, the soleus muscles were unloaded for 7 days by hindlimb suspension. Subsequent reloading was provoked by allowing the animals to return to normal cage activity for 1 day. The muscle was isolated, snap frozen and total RNA extracted


title: FAK transfected rat soleus muscle 432, unloaded + one day reloaded


title: FAK transfected rat soleus muscle 420, unloaded + one day reloaded


title: HF-16980 15220_Hind

tag: Tumor


title: FAK transfected rat soleus muscle 419, unloaded + one day reloaded


title: HF-17267 16444_Hind

tag: Somatic


title: FAK transfected rat soleus muscle 433, unloaded + one day reloaded


title: empty transfected rat soleus muscle 419, unloaded + one day reloaded


title: FAK transfected rat soleus muscle 418, unloaded + one day reloaded


title: empty transfected rat soleus muscle 420, unloaded + one day reloaded


title: empty transfected rat soleus muscle 418, unloaded + one day reloaded


title: Tumor_1sty

status: Public on Mar 18 2010

city: Providence

first: Graham

middle: M

last: Poage

state: RI

address: 70 Ship St

institute: Brown University

description:
Tumor ID 101
Hybridized to 250K_Sty.

hyb_protocol: As per manufacturer (Affymetrix).

scan_protocol: As per manufacturer (Affymetrix).

data_processing:
Data were collected at the Harvard Partners Microarray Core Facility. Inferred copy number states of each SNP were extracted and converted from .CEL files into signal intensities using GCOS and Affymetrix Copy Number Analysis Tool (CNAT) v4.0.1. We utilized the HMM-based algorithm with defaults for tuning parameters, Gaussian smoothing, transition decay, and median scaling.

The 'GSE20939_tumor_copy_number.txt' file, which is linked to the Series GSE20939 record as a supplementary file, contains the (blood-adjusted) tumor copy number calls used in our final analyses.

source_name: head and neck tumor_1

label_protocol: As per manufacturer (Affymetrix).

growth_protocol: Fresh-frozen human tissue.

extract_protocol: Qiagen Qiamp DNA extraction kit.

treatment_protocol: None.

value: head and neck squamous cell carcinoma

tag: tumor site

value: oral

tag: tumor id


title: empty transfected rat soleus muscle 429-430, unloaded

description: CMV-driven empty expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 2 days after transfection the soleus muscles were unloaded for 7 days by hindlimb suspension. The muscle was isolated, snap frozen and total RNA extracted


title: FAK transfected rat soleus muscle 427-428, unloaded

description: CMV-driven FAK expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 2 days after transfection the soleus muscles were unloaded for 7 days by hindlimb suspension. The muscle was isolated, snap frozen and total RNA extracted


title: FAK transfected rat soleus muscle 429-430, unloaded


title: HF-17203 16440_Hind


title: empty transfected rat soleus muscle 427-428, unloaded


title: FAK transfected rat soleus muscle 424, unloaded + 5 days reloaded

description: CMV-driven FAK expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 2 days after transfection, the soleus muscles were unloaded for 7 days by hindlimb suspension. Subsequent reloading was provoked by allowing the animals to return to normal cage activity for 5 days. The muscle was isolated, snap frozen and total RNA extracted


title: empty transfected rat soleus muscle, unloaded


title: FAK transfected rat soleus muscle 423, unloaded


title: FAK transfected rat soleus muscle 442, cage control

description: CMV-driven FAK expression construct and empty construct were electro-transferred into a soleus muscle of an anesthetized rat. 7 days after overexpression, the muscle was isolated, snap frozen and total RNA extracted


title: FAK transfected rat soleus muscle 422, unloaded


title: FAK transfected rat soleus muscle 422, cage control and inhibitor

description: CMV-driven FAK expression construct and FRNK construct were electro-transferred into a soleus muscle of an anesthetized rat. 7 days after overexpression, the muscle was isolated, snap frozen and total RNA extracted


title: empty transfected rat soleus muscle 423, unloaded


title: FAK transfected rat soleus muscle 441, cage control


title: FAK transfected rat soleus muscle 441 cage control and inhibitor


title: FAK transfected rat soleus muscle 438, cage control and inhibitor


title: FAK transfected rat soleus muscle 438-2, cage control and inhibitor


title: FAK transfected rat soleus muscle 440, cage control and inhibitor


title: FAK transfected rat soleus muscle, cage control and inhibitor


title: HF-17267 16453_Xba


title: FAK transfected rat soleus muscle 437-2, cage control


title: FAK transfected rat soleus muscle 437, cage control


title: FAK transfected rat soleus muscle 411, cage control

description: CMV-driven FAK expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 7 days after overexpression, the muscle was isolated, snap frozen and total RNA extracted


title: FAK transfected rat soleus muscle 440, cage control


title: empty transfected rat soleus muscle 405, cage control

description: CMV-driven empty expression construct was electro-transferred into a soleus muscle of an anesthetized rat. 7 days after overexpression, the muscle was isolated, snap frozen and total RNA extracted


title: empty transfected rat soleus muscle 409, cage control


title: FAK transfected rat soleus muscle 409, cage control


title: FAK transfected rat soleus muscle 408, cage control


title: FAK transfected rat soleus muscle 439, cage control


title: FAK transfected rat soleus muscle, cage control


title: empty transfected rat soleus muscle 410, cage control


title: empty transfected rat soleus muscle 411, cage control


title: FAK transfected rat soleus muscle 410, cage control


title: empty transfected rat soleus muscle 408, cage control


title: Flooded Sicot 71 root tissue biological rep 1

status: Public on Dec 18 2009

city: Acton

first: Jed

last: Christianson

state: ACT

address: Clunies Ross Road

country: Australia

institute: CSIRO Plant Industry

description: plants were grown in the glass house to the two-leaf stage prior to treatment

hyb_protocol: Following fragmentation, cRNA was hybridized to the Cotton Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix genechip scanner 3000 7G

data_processing: The data analysed using the limma Bioconductor package in R. Array data was normalized using the EXPRESSO function (Gautier et al., 2005). A robust multi-chip average was calculated using quantile normalization, background correction and the median polish method as recommended by (Bolstad et al., 2003) and (Irizarry et al., 2003).

organism: Gossypium hirsutum

source_name: Whole root, flooded 4 hrs.

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 7 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: Plants were grown in soil mixture in the glasshouse under seasonal lighting conditons for Canberra, ACT, Australia in September 2007 and watered daily

extract_protocol: Plant tissues were flash frozen and ground in liquid nitrogen. Total RNA was extracted using a hot borate buffer method as described in Cadman et al, 2006, Plant Journal, 46: 805-822

treatment_protocol: Plants were either left as they had been growing or flooded with water so that the entire root system below the hypocotyl was submerged

tag: stress

value: flooded

tag: time

value: 4 hrs.

tag: cultivar

value: Sicot 71

value: whole root


title: Flooded Sicot 71 leaf tissue biological rep 1

source_name: First leaf, flooded 24 hrs.

value: 24 hrs.

value: first leaf


title: Control Sicot 71 leaf tissue biological rep 2

source_name: First leaf, control

value: control


title: Control Sicot 71 root tissue biological rep 2

source_name: Whole root, control


title: FAK transfected rat soleus muscle 405, cage control


title: Control Sicot 71 root tissue biological rep 1


title: Control Sicot 71 leaf tissue biological rep 1


title: Flooded Sicot 71 leaf tissue biological rep 2


title: MEF, 10h TGF-β1 treatment, wild type 2

status: Public on Nov 05 2009

city: Lausanne

first: Milos

last: Pjanic

state: VD

address: EPFL CH B1 426 Station 6

department: Institute of Biotechnology

institute: Faculty of Biology and Medicine, University of Lausanne

description: gene expression data from 10h TGF-β1 treated wild type cells

hyb_protocol: Affymetrix Mouse Genome 430 2.0 arrays were hybridized with 11 micrograms of labeled, amplified cRNA , washed, stained and scanned according to the protocol described in Affymetrix GeneChip® Expression Analysis Manual (Fluidics protocol EukGeWS2v5_450).

scan_protocol: Scanning was done on an Affymetrix GeneChip Scanner 7G.

data_processing: Normalized expression signals were calculated from Affymetrix CEL files using RMA (Irizarry et al., 2003).

organism: Mus musculus

source_name: mouse embryonic fibroblasts, 10h TGF-β1 treatment, from wild type embryo n 2

label_protocol: Biotinylated cRNA was prepared from 3 ug of total RNS and was performed using the GeneChip® One-Cycle cDNA Synthesis kits according to the manufacturers' protocols (Affymetrix, Santa Clara, CA, USA). Labeling, hybridization and scanning of the samples were performed as described by Affymetrix (http://www.affymetrix.com).

growth_protocol: Primary mouse embryonic fibroblasts were isolated from 14-day-old embryos. The head and the liver were removed and the remaining embryonic tissues were finely minced and digested by incubation in 0.05% trypsin-EDTA solution. Isolated cells were cultured in DMEM supplemented with 10% FCS at 37°C and 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions. Further purification of RNA was performed using RNeasy Mini Kits (Qiagen).

treatment_protocol: Fibroblasts isolated from 3 wild-type and 3 knock-out mice were cultured in triplicate and after incubation for 4-6h with DMEM supplemented with 1% AlbuMAX II, 1% Insulin/Transferrin/Selenium mix, MEFs were incubated with 12.5 ng/ml of TGF-β1(PerproTech EC)  for 1h or 10h, or they were left untreated.

tag: cell type

value: fibroblasts from 14 day-old embryo

tag: genotype

value: wild type

tag: treatment

value: 10 hours


title: MEF, 10h TGF-β1 treatment, knock out 3

description: gene expression data from 10h TGF-β1 treated NFI-C knock out cells

source_name: mouse embryonic fibroblasts, 10h TGF-β1 treatement, from NFI-C knock out embryo n 3

value: NFI-C knock out


title: MEF, 1h TGF-β1 treatment, knock out 3

description: gene expression data from 1h TGF-β1 treated NFI-C knock out cells

source_name: mouse embryonic fibroblasts, 1h TGF-β1 treatement, from NFI-C knock out embryo n 3

value: 1 hour


title: MEF, 10h TGF-β1 treatment, wild type 1

source_name: mouse embryonic fibroblasts, 10h TGF-β1 treatment, from wild type embryo n 1


title: MEF, no treatment, knock out 1

description: gene expression data from NFI-C knock out cells

source_name: mouse embryonic fibroblasts, basal level, from NFI-C knock out embryo n 1


title: MEF, 1h TGF-β1 treatment, wild type 2

description: gene expression data from 1h TGF-β1 treated wild type cells

source_name: mouse embryonic fibroblasts, 1h TGF-β1 treatment, from wild type embryo n 2


title: MEF, 1h TGF-β1 treatment, wild type 3

source_name: mouse embryonic fibroblasts, 1h TGF-β1 treatment, from wild type embryo n 3


title: MEF, 10h TGF-β1 treatment, knock out 2

source_name: mouse embryonic fibroblasts, 10h TGF-β1 treatement, from NFI-C knock out embryo n 2


title: MEF, no treatment, knock out 3

source_name: mouse embryonic fibroblasts, basal level, from NFI-C knock out embryo n 3


title: MEF, no treatment, knock out 2

source_name: mouse embryonic fibroblasts, basal level, from NFI-C knock out embryo n 2


title: MEF, 10h TGF-β1 treatment, knock out 1

source_name: mouse embryonic fibroblasts, 10h TGF-β1 treatement, from NFI-C knock out embryo n 1


title: MEF, 1h TGF-β1 treatment, knock out 2

source_name: mouse embryonic fibroblasts, 1h TGF-β1 treatement, from NFI-C knock out embryo n 2


title: MEF, 1h TGF-β1 treatment, wild type 1

source_name: mouse embryonic fibroblasts, 1h TGF-β1 treatment, from wild type embryo n 1


title: MEF, 10h TGF-β1 treatment, wild type 3

source_name: mouse embryonic fibroblasts, 10h TGF-β1 treatment, from wild type embryo n 3


title: Flooded Sicot 71 root tissue biological rep 2

source_name: Whole root, flooded 4 hrs.


title: empty transfected rat soleus muscle, cage control

source_name: Martin Flueck, Institute of Anatomy, University of Berne

value: soleus muscle

value: 3 month


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

status: Public on Nov 03 2009

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 75 (min) after ϕYS40 infection 1

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

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

data_processing: The expression levels were summarized by one-step Tukey’s biweight algorithm using GeneChip Operating Software, version 1.2 (Affymetrix, Santa Clara, CA).

organism: Thermus thermophilus HB8

source_name: T. thermophilus HB8, (-)crp, rich medium, 75 (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 75 (min) after the infection (OD600nm = ~ 1.96).

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

tag: protocol

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


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

source_name: T. thermophilus HB8, (-)crp, rich medium, 100 (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 100 (min) after the infection (OD600nm = ~ 2.60).

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


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

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: (-)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, 100 (min) time point after phage ϕYS40 infection (3)

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

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).


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

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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 100 (min) after the infection (OD600nm = ~ 2.65).

value: wild-type

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


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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 100 (min) after the infection (OD600nm = ~ 2.14).


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

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

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 = ~ 0.69).

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


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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 100 (min) after the infection (OD600nm = ~ 2.68).


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

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

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: MEF, no treatment, wild type 2

description: gene expression data from wild type cells

source_name: mouse embryonic fibroblasts, basal level, from wild type embryo n 2


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

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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 75 (min) after the infection (OD600nm = ~ 2.00).

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


title: MEF, no treatment, wild type 3

source_name: mouse embryonic fibroblasts, basal level, from wild type embryo n 3


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

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

growth_protocol: The T. thermophilus HB8 (-)csp 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).


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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 75 (min) after the infection (OD600nm = ~ 2.14).


title: Wildtype early stationary

status: Public on Nov 17 2009

city: Leuven

first: Kristof

last: Engelen

address: Kasteelpark Arenberg 20

country: Belgium

institute: KULeuven

description: Wild-type R. etli CFN42 was grown at 30˚C in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken 6 hours after reaching the maximum OD, representing early stationary phase.

hyb_protocol: The Cy3-labeled cDNA was hybridized to the custom R. etli tiling expression array at 42°C for 16 hour using the NimbleGen Hybridization System and kit.

scan_protocol: GenePix 4000B.

data_processing: Data preprocessing was done by performing a nonlinear intensity dependent rescaling on non-background corrected data. To this end, a loess fit normalization with a span of 25% was performed for each array compared against an artificial reference array, consisting of the median intensity values of each probe across all arrays. To ensure that the artificial reference itself was not altered by this rescaling, the artificial reference expression levels were chosen for the average log intensity in the loess fit (instead of the mean expression levels of the respective array and the artificial reference). A robust median-polish procedure was used to combine measurements from multiple probes into a single value. Results are linked as supplementary GFF files in standard format with columns: seqname (chromosome name); source (article); feature (RNA); start; end; score (normalized expression value); strand (left empty); frame (empty for RNA); attribute (ID).

organism: Rhizobium etli CFN 42

source_name: Wildtype R. etli CFN42 6 hours after reaching the maximum OD

label_protocol: cDNA, median≥400bp, was synthesized using random decamers (Ambion) and the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen) according to the manufacturer’s protocol. All cDNA samples were labeled with Cy3 by Nimblegen using the NimbleGen One- Color DNA Labeling Kit (05223555001).

extract_protocol: Total RNA was extracted using the TRIzol Plus RNA Purification kit (Invitrogen). Cells were resuspended in 1 ml of TRIzol and shaken twice by a Precellys 24 (Bertin Technologies) at 6500 rpm for 45 seconds with 0.25 ml of 0.1 mm glass beads before following the manufacturer’s instructions. Phase Lock Gel tubes (heavy type) were used to efficiently separate the organic and aqueous phase. DNA contamination was removed by two treatments of 2 μl TURBO DNase (Ambion) and afterwards checked by PCR (45 cycles). To increase RNA yields and account for experimental variation, RNA from 6 different free-living cultures was pooled. RNA was precipitated in 3 volumes of isopropanol and 1/10 volume of sodium acetate, washed twice in ethanol and dissolved in nuclease-free ultrapure water. RNA integrity was analyzed using Experion RNA StdSens Chips (Biorad, Hercules, CA, before and after precipitation ). The sample had an RNA Quality Indicator value of 10. The ncRNA peak could be detected in each sample. RNA quantity and purity was assessed using the NanoDrop ND-1000. The A260/A280 ratio and A260/A230 ratio was ≥ 2.

tag: genetic background

value: CFN 42


title: Wildtype early exponential

description: Wild-type R. etli CFN42 was grown at 30˚C in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at OD600 = 0.3, representing early exponential phase.

source_name: Wildtype R. etli CFN42 at OD600 = 0.3


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

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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 50 (min) after the infection (OD600nm = ~ 1.50).

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


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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 50 (min) after the infection (OD600nm = ~ 1.60).


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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 75 (min) after the infection (OD600nm = ~ 2.02).


title: Bacteroids three weeks

description: R. etli CFN42 was grown at 30˚C in AMS medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Bacteroid samples were obtained from nodules 3 weeks after inoculation of Common bean plants (Phaseolus vulgaris cv Limburgse vroege).

data_processing: Data preprocessing was done by performing a nonlinear intensity dependent rescaling on non-background corrected data. To this end, a loess fit normalization with a span of 25% was performed for each array compared against an artificial reference array, consisting of the median intensity values of each probe across all arrays. To ensure that the artificial reference itself was not altered by this rescaling, the artificial reference expression levels were chosen for the average log intensity in the loess fit (instead of the mean expression levels of the respective array and the artificial reference). A robust median-polish procedure was used to combine measurements from multiple probes into a single value. Results are linked as supplementary GFF files in standard format with columns: seqname (chromosome name); source (article); feature (RNA); start; end; score (normalized value); strand (forward (1) or reverse (-1)); frame (empty for RNA); attribute (ID).

source_name: Wildtype R. etli CFN42 bacteroids harvested 3 weeks after inoculation

extract_protocol: Total RNA was extracted using the TRIzol Plus RNA Purification kit (Invitrogen). Bacteroid pellets were resuspended in 1 ml of TRIzol and shaken twice by a Precellys 24 (Bertin Technologies) at 6500 rpm for 45 seconds with 0.25 ml of 0.1 mm glass beads before following the manufacturer’s instructions. Phase Lock Gel tubes (heavy type) were used to efficiently separate the organic and aqueous phase. DNA contamination was removed by two treatments of 2 μl TURBO DNase (Ambion) and afterwards checked by PCR (45 cycles). ). To increase RNA yields and account for experimental variation, RNA from 6 different free-living cultures was pooled. Bacteroid RNA was obtained after crushing 10g nodules of 25 plants using liquid nitrogen. RNA was precipitated in 3 volumes of isopropanol and 1/10 volume of sodium acetate, washed twice in ethanol and dissolved in nuclease-free ultrapure water. RNA integrity was analyzed using Experion RNA StdSens Chips (Biorad, Hercules, CA, before and after precipitation ). The sample had an RNA Quality Indicator value of 10. The ncRNA peak could be detected in each sample. RNA quantity and purity was assessed using the NanoDrop ND-1000. The A260/A280 ratio and A260/A230 ratio was ≥ 2.


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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 50 (min) after the infection (OD600nm = ~ 1.66).


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

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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 25 (min) after the infection (OD600nm = ~ 1.26).

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


title: NPC16

city: Durham

first: Wenbin

last: Wei

address: Stockton Road

department: Biosciences

country: United Kingdom

institute: Durham University

description: Stage III, T2, N2, M0, G4

hyb_protocol: Affymetrix Standard protocol

scan_protocol: Affymetrix Standard protocol

data_processing: The scanned images of microarray chips were analyzed using the Affymetrix GenChip Operating Software (GCOS) with the default settings except that the target signal was set to 100.

source_name: biopsy of undifferentiated NPC

label_protocol: The cDNA was synthesized, in vitro transcribed and labeled using standard Affymetrix protocols.

extract_protocol: RNA was extracted from biopsy samples using TRIzol Reagent (Invitrogen, USA) and purified by the RNeasy Mini Kit (Qiagen, UK).

tag: disease state

value: Nasopharyngeal carcinoma

tag: stage


title: NPC17

description: Stage III, T3, N2, M0, G4


title: MEF, no treatment, wild type 1

source_name: mouse embryonic fibroblasts, basal level, from wild type embryo n 1

growth_protocol: Primary mouse embryonic fibroblasts were isolated from 14-day-old embryos. The head and the liver were removed and the remaining embryonic tissues were finely minced and digested by incubation in 0.05% trypsin-EDTA solution. Isolated cells were cultured in DMEM supplemented with 10% FCS at 37°C and 5% CO2.

value: fibroblasts from 14 day-old embryo

value: wild type


title: MEF, 1h TGF-β1 treatment, knock out 1

description: gene expression data from 1h TGF-β1 treated NFI-C knock out cells

source_name: mouse embryonic fibroblasts, 1h TGF-β1 treatement, from NFI-C knock out embryo n 1

value: NFI-C knock out


title: duodenum at E16.5, biological rep3

status: Public on Oct 01 2009

city: Ann Arbor

first: Xing

last: Li

state: MI

address: 109 Zina Pitcher Place,045 BSRB

department: Bioinformatics Program & CDB

institute: Universtiy of Michigan

description: Gene expression data from duodenum tissue close to pylorus from E16.5 mouse embryo

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized  to MOE 430.2 microarrays (eighteen total chips: six time/tissue groups, three replicate chips for each group; Affymetrix, Santa Clara, CA) by the University of Michigan Cancer Center Microarray Core Facility. . GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The .DAT files were obtained by Affymetrix GCOS software. Then the .CEL files were analyzed using Robust Muti-array Average (RMA) for background adjustment, normalization and summrization to obtain gene expression data matrix.

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: Embryos from C57Bl/6J mice were collected from timed pregnant females, with the day of vaginal plug detection considered day 0.5. Intestine and stomach were removed and three contiguous segments were collected from antrum (stomach), pylorus, and duodenum.

extract_protocol: Total RNA was isolated with TRIzol (Invitrogen, Carlsbad, CA) and purified using the RNeasy kit (Qiagen, Valencia, CA), per the manufacturers’ instructions. Separate collections were performed for RT-PCR validation of microarray results.

treatment_protocol: For the microarray experiment, a total of 174 E14.5 embryos and 95 E16.5 embryos were dissected, and for each time/tissue group (eg, E14.5 duodenum; six groups total), collected tissue was randomly pooled into one of three samples for replicate analysis.

tag: tissue

value: duodenum

tag: age

tag: developmental stage

value: embryo


title: pylorus at E16.5, biological rep2

description: Gene expression data from pylorus tissue from E16.5 mouse embryo

source_name: pylorus tissue from E16.5 mouse embryo

value: pylorus

tag: strain


title: pylorus at E16.5, biological rep3


title: Wildtype late exponential

description: Wild-type R. etli CFN42 was grown at 30˚C in acid minimal salts medium supplied with 10 mM NH4Cl and 10 mM succinate while monitoring the optical density (OD) of the culture. Samples were taken at OD600 = 0.7, representing late exponential phase.

source_name: Wildtype R. etli CFN42 at OD600 = 0.7

extract_protocol: Total RNA was extracted using the TRIzol Plus RNA Purification kit (Invitrogen). Cells were resuspended in 1 ml of TRIzol and shaken twice by a Precellys 24 (Bertin Technologies) at 6500 rpm for 45 seconds with 0.25 ml of 0.1 mm glass beads before following the manufacturer’s instructions. Phase Lock Gel tubes (heavy type) were used to efficiently separate the organic and aqueous phase. DNA contamination was removed by two treatments of 2 μl TURBO DNase (Ambion) and afterwards checked by PCR (45 cycles). To increase RNA yields and account for experimental variation, RNA from 6 different cultures or 4 batches of bacteroids was pooled. RNA was precipitated in 3 volumes of isopropanol and 1/10 volume of sodium acetate, washed twice in ethanol and dissolved in nuclease-free ultrapure water. RNA integrity was analyzed using Experion RNA StdSens Chips (Biorad, Hercules, CA, before and after precipitation ). The sample had an RNA Quality Indicator value of 10. The ncRNA peak could be detected in each sample. RNA quantity and purity was assessed using the NanoDrop ND-1000. The A260/A280 ratio and A260/A230 ratio was ≥ 2.


title: duodenum at E16.5, biological rep2

source_name: duodenum tissue close to pylorus from E16.5 mouse embryo


title: duodenum at E14.5, biological rep3

description: Gene expression data from duodenum tissue close to pylorus from E14.5 mouse embryo


title: pylorus at E14.5, biological rep2

description: Gene expression data from pylorus tissue from E14.5 mouse embryo

source_name: pylorus tissue from E14.5 mouse embryo


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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 25 (min) after the infection (OD600nm = ~ 0.98).


title: stomach at E16.5, biological rep1

description: Gene expression data from stomach tissue close to pylorus from E16.5 mouse embryo

value: stomach


title: stomach at E14.5, biological rep1

description: Gene expression data from stomach tissue close to pylorus from E14.5 mouse embryo


title: stomach at E14.5, biological rep2

source_name: stomach tissue close to pylorus from E14.5 mouse embryo


title: pylorus at E14.5, biological rep3


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

description: wild-type strain ϕYS40 pre-infection 1

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

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 (OD600nm = ~ 0.73).

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


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

description: wild-type strain ϕYS40 pre-infection 3

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 (OD600nm = ~ 0.74).


title: stomach at E14.5, biological rep3


title: stomach at E16.5, biological rep2

source_name: stomach tissue close to pylorus from E16.5 mouse embryo


title: duodenum at E14.5, biological rep1

source_name: duodenum tissue close to pylorus from E14.5 mouse embryo


title: pylorus at E16.5, biological rep1


title: duodenum at E16.5, biological rep1


title: pylorus at E14.5, biological rep1


title: duodenum at E14.5, biological rep2


title: 1308

city: New York

first: Edgar

middle: D.

last: Charles

state: NY

address: 1230 York Avenue, Box 64

department: Virology and Infectious Disease

institute: Rockefeller University

hyb_protocol: Illumina Hybridization protocol performed at 48 C

scan_protocol: Illumina BeadChip Protocol

data_processing:
The GeneSpring normalization procedure was as follows:
Threshold raw signals were set to 1.0.
Raw signals were scaled to the 50th percentile.
Baseline transformation was not applied.

source_name: peripheral IgM+CD27+ B Cell

label_protocol: UNG biotinylation

extract_protocol: Rneasy Plus Micro Kit (QIAgen); NUGEN WT-Ovation Amplification

tag: hcvab+

value: Y

tag: hcv rna+

tag: igm mc+


title: stomach at E16.5, biological rep3


title: 1432


title: 1540


title: 1716


title: 92200


title: 1419

value: N


title: 1116


title: 880


title: LDU 107


title: ECH 531


title: 1403


title: ECH 522


title: ECH 535


title: ECH 516


title: 1330


title: ECH 519


title: ECH 532


title: 1235


title: ECH 529


title: ECH 520


title: 543


title: LDU 099


title: 856


title: 731


title: 1154


title: 1864


title: ECH 530


title: 1197


title: ECH 533


title: ECH 503


title: ECH 527


title: ECH 521


title: ECH 528


title: 1 cGy irradiation of shGATA3 keratinocytes 24h

status: Public on Sep 15 2009

city: LYON

first: Jerome

last: Lamartine

address: 7 passage du Vercors

country: France

institute: Université Lyon I

description: Hybridization irradiated vs control

hyb_protocol: Direct hybridization sample (Cy5 vs Cy3)

scan_protocol: Axon 4000B Genepix software

data_processing: Genepix software normalization

molecule: polyA RNA

source_name: 1 cGy irradiated shGATA3 keratinocytes 24h

label_protocol: Ambion / Amino Allyl MessageAmp II aRNA kit

extract_protocol: Qiagen / microRNAeasy kit

value: Human foreskin

tag: gender

value: Male

value: 24 hr

tag: genotype/variation

value: shGATA3 knock-down

value: 1 cGy

source_name: 0 cGy irradiated shGATA3 keratinocytes 24h

value: 0 cGy


title: 1 cGy irradiation of shSCR keratinocytes 72h swap

description: Hybridization irradiated vs control

source_name: 0 cGy irradiated shSCR keratinocytes 72h

tag: time

value: 72 hr

value: shSCR knock-down (control)

source_name: 1 cGy irradiated shSCR keratinocytes 72h


title: 1 cGy irradiation of shSCR keratinocytes 72h

description: Hybridization irradiated vs control


title: 1 cGy irradiation of shGATA3 keratinocytes 4h

description: Hybridization irradiated vs control

source_name: 1 cGy irradiated shGATA3 keratinocytes 4h

value: 4 hr

source_name: 0 cGy irradiated shGATA3 keratinocytes 4h


title: 1 cGy irradiation of shGATA3 keratinocytes 72h swap

description: Hybridization irradiated vs control

source_name: 0 cGy irradiated shGATA3 keratinocytes 72h

source_name: 1 cGy irradiated shGATA3 keratinocytes 72h


title: 1 cGy irradiation of shGATA3 keratinocytes 72h

description: Hybridization irradiated vs control


title: 1 cGy irradiation of shGATA3 keratinocytes 48h

description: Hybridization irradiated vs control

source_name: 1 cGy irradiated shGATA3 keratinocytes 48h

value: 48 hr

source_name: 0 cGy irradiated shGATA3 keratinocytes 48h


title: 1 cGy irradiation of shGATA3 keratinocytes 24h swap

description: Hybridization irradiated vs control


title: 1 cGy irradiation of shSCR keratinocytes 24h swap

description: Hybridization irradiated vs control

source_name: 0 cGy irradiated shSCR keratinocytes 24h

source_name: 1 cGy irradiated shSCR keratinocytes 24h


title: 1 cGy irradiation of shSCR keratinocytes 24h

description: Hybridization irradiated vs control


title: 1 cGy irradiation of shSCR keratinocytes 4h

description: Hybridization irradiated vs control

source_name: 1 cGy irradiated shSCR keratinocytes 4h

source_name: 0 cGy irradiated shSCR keratinocytes 4h


title: Cv 8d-2

status: Public on Sep 11 2009

city: Aberdeen

first: Denise

last: Kelly

address: Institute of Medical Sciences

institute: University of Aberdeen

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

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

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

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

label: Biotin

source_name: ileal tissue, Cv 8d

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

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

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

treatment_protocol: Cv female 8-9-week-old mice were sacrificed on d8 post-colonization as age-match to GF, Cvd, Hum and SFB mice.

tag: culture

value: Cv 8d

value: female

value: 8-9 weeks

value: ileum


title: SFB 8d-3

source_name: ileal tissue, SFB 8d

treatment_protocol: GF female 8-9-week-old mice were gavaged twice at a 24-hr interval with 0.5 mL of fresh anaerobic cultures of fecal homogenate from SFB mono-associated mice, and sacrificed on d8 post-colonization as age-match to Cv, GF, Hum and SFB mice.

value: SFB 8d


title: Cv 60d-3

source_name: ileal tissue, Cv 60d

treatment_protocol: Cv female 8-9-week-old mice were sacrificed on d60 post-colonization as age-match to GF, Cvd, Hum and SFB mice.

value: Cv 60d


title: Cv 60d-2


title: SFB 8d-1


title: Cv 8d-3


title: 1 cGy irradiation of shGATA3 keratinocytes 48h swap

description: Hybridization irradiated vs control


title: 1 cGy irradiation of shSCR keratinocytes 4h swap

description: Hybridization irradiated vs control


title: SFB 60d-1

source_name: ileal tissue, SFB 60d

treatment_protocol: GF female 8-9-week-old mice were gavaged twice at a 24-hr interval with 0.5 mL of fresh anaerobic cultures of fecal homogenate from SFB mono-associated mice, and sacrificed on d60 post-colonization as age-match to Cv, GF, Hum and SFB mice.

value: SFB 60d


title: 1 cGy irradiation of shSCR keratinocytes 48h swap

description: Hybridization irradiated vs control

source_name: 0 cGy irradiated shSCR keratinocytes 48h

value: Human foreskin

source_name: 1 cGy irradiated shSCR keratinocytes 48h


title: SFB 8d-2


title: SFB 60d-2


title: SFB 60d-3


title: Cv 8d-1


title: Cv 60d-1


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

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

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

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. Cells infected with ϕYS40 bacteriophage and harvested at 25 (min) after the infection (OD600nm = ~ 1.38).

tag: genotype

value: wild-type

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


title: Hum 8d-3

source_name: ileal tissue, Hum 8d

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

value: Hum 8d


title: Hum 60d-1

source_name: ileal tissue, Hum 60d

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

value: Hum 60d


title: 1 cGy irradiation of shGATA3 keratinocytes 4h swap

description: Hybridization irradiated vs control

source_name: 0 cGy irradiated shGATA3 keratinocytes 4h

value: Male

value: shGATA3 knock-down

tag: treatment

value: 0 cGy

source_name: 1 cGy irradiated shGATA3 keratinocytes 4h

value: 1 cGy


title: Cvd 8d-2

source_name: ileal tissue, Cvd 8d

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

value: Cvd 8d


title: Cvd 60d-1

source_name: ileal tissue, Cvd 60d

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

value: Cvd 60d


title: Hum 60d-2

value: female


title: Cvd 8d-3

value: 8-9 weeks


title: Cvd 60d-3

value: ileum


title: Cvd 60d-2


title: Hum 8d-1


title: 1 cGy irradiation of shSCR keratinocytes 48h dual

description: Hybridization irradiated vs control

value: 48 hr

value: shSCR knock-down (control)


title: Ag-B7+TSA @72hr, biological rep1

status: Public on Jul 22 2009

city: Minneapolis

first: PUJYA

last: AGARWAL

state: MN

address: 6-246 NHH, 312 Church Street, SE

department: Laboratory,Medicine and Pathology

institute: University of Minnesota

description: OT-I CD8 T cells stimulated with Ag-B7+TSA @72hr, biological rep1

hyb_protocol: Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45oC on Murine GeneChip U74Av2 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400 according to Affymetrix protocol at the University of Minnesota Microarray facility.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings as the normalization method with scaling target signal set to 1000.

source_name: In vitro stimulated OT-I TCR transgenic CD8 T lymphocytes

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 10ug total RNA (Expression Analysis Technical Manual, Affymetrix) using Enzo Bioarray HighYield RNA transcript labeling kit.

growth_protocol: CD44lo CD8+ T cells were negatively enriched from lymph nodes of OT-1 transgenic mice and stimulated in vitro with H-2Kb:SINNFEKL complex and B7-1 proteins coated on 5uM latex microspheres in presence or absence of murine rIL-12, universal type I IFN or trichostatin A. All cultures were supplemented with human rIL-2.  At 0h, 24h, 48h, and 72h the cells from cultures were harvested.

extract_protocol: Total RNA was extracted using Rneasy Mini Kit, Qiagen and performed according to the manufacturer's instructions.

treatment_protocol: At indicated times after stimulation, the cells were harvested, washed with PBS and subjected to RNA isolation procedure.

tag: cell type

value: CD8 T lymphocyte

value: OT-1 TCR transgenic

value: 6 to 8 weeks

tag: naive or stimulated

value: stimulated

tag: stimulating agent

tag: time point

tag: biological rep


title: GF 8d-2

source_name: ileal tissue, GF 8d

treatment_protocol: Germfree (GF) mice were sacrificed on d8 post-colonization as age-match to Cv, Cvd, Hum and SFB mice.

value: GF 8d

tag: age

tag: tissue


title: GF 60d-2

source_name: ileal tissue, GF 60d

treatment_protocol: Germfree (GF) mice were sacrificed on d60 post-colonization as age-match to Cv, Cvd, Hum and SFB mice.

value: GF 60d

tag: strain


title: Ag-B7+IL12 @72hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7+IL12 @72hr, biological rep1


title: Cvd 8d-1


title: Ag-B7+IFNa/b @72hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7+IFNa/b @72hr, biological rep1


title: GF 60d-1


title: Ag-B7+IFNa/b @48hr, biological rep2

description: OT-I CD8 T cells stimulated with Ag-B7+IFNa/b @48hr, biological rep2


title: GF 60d-3


title: Ag-B7+IFNa/b @48hr, biological rep3

description: OT-I CD8 T cells stimulated with Ag-B7+IFNa/b @48hr, biological rep3


title: Ag-B7+IL12 @48hr, biological rep3

description: OT-I CD8 T cells stimulated with Ag-B7+IL12 @48hr, biological rep3


title: Ag-B7+IL12 @48hr, biological rep2

description: OT-I CD8 T cells stimulated with Ag-B7+IL12 @48hr, biological rep2


title: Naïve @ 0hr, biological rep3

description: Naïve OT-I CD8 T cells stimulated @ 0hr, biological rep3

source_name: Naive OT-I TCR transgenic CD8 T lymphocytes

value: naive


title: GF 8d-3


title: Ag-B7@ 24hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7@ 24hr, biological rep1


title: Ag-B7@ 48hr, biological rep2

description: OT-I CD8 T cells stimulated with Ag-B7@ 48hr, biological rep2


title: Ag-B7+IFNa/b @48hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7+IFNa/b @48hr, biological rep1


title: GF 8d-1


title: Ag-B7@ 48hr, biological rep4

description: OT-I CD8 T cells stimulated with Ag-B7@ 48hr, biological rep4


title: T 3

status: Public on Jul 01 2009

city: Milan

first: Maya

last: Fedeli

address: via Olgettina 58

department: DIBIT

country: Italy

institute: San Raffaele Scientific Institute

description: microRNA expression

hyb_protocol: The Hy3™-labeled samples and a Hy5™-labeled reference RNA sample were mixed pair-wise and hybridized to the miRCURY™ LNA array version 11.0 (Exiqon, Denmark), which contains capture probes targeting all miRNAs for human, mouse or rat registered in the miRBASE version 12.0 at the Sanger Institute. The hybridization was performed according to the miRCURY™ LNA array manual using a Tecan HS4800 hybridization station (Tecan, Austria).

scan_protocol: Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and the image analysis was carried out using the ImaGene 8.0 software (BioDiscovery, Inc., USA).

data_processing: The quantified signals were background corrected (Normexp with offset value 10 – Ritchie et al., 2007) and normalized using the global Lowess (LOcally WEighted Scatterplot Smoothing) regression algorithm.

source_name: T 3

label_protocol: miRCURY LNA Array power labeling kit (Exiqon, Denmark)

extract_protocol: miRVana kit (Ambion)

treatment_protocol: Enrichment of HSA low mature thymocytes by anti-HSA mAb and rabbit complement; sorting of mature NKT and T cells

value: T cell

value: 4 weeks

value: 18 pooled thymi

source_name: Total thymocytes

value: 18 pooled thymi X 3 replicates; pool of all the thymi used in the sortings; used as a common reference


title: T 1

description: microRNA expression

source_name: T 1


title: Naïve @ 0hr, biological rep2

description: Naïve OT-I CD8 T cells stimulated @ 0hr, biological rep2


title: Ag-B7@ 48hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7@ 48hr, biological rep1


title: Ag-B7+IL12 @48hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7+IL12 @48hr, biological rep1


title: NKT 3

description: microRNA expression

source_name: NKT 3

value: NKT cell


title: Ag-B7+IL12 @24hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7+IL12 @24hr, biological rep1


title: NKT 1

description: microRNA expression

source_name: NKT 1


title: Ag-B7+IFNa/b @24hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7+IFNa/b @24hr, biological rep1


title: Ag-B7@ 72hr, biological rep1

description: OT-I CD8 T cells stimulated with Ag-B7@ 72hr, biological rep1


title: NKT 2

description: microRNA expression

source_name: NKT 2


title: Ag-B7@ 48hr, biological rep3

description: OT-I CD8 T cells stimulated with Ag-B7@ 48hr, biological rep3


title: Naïve @ 0hr, biological rep1

description: Naïve OT-I CD8 T cells stimulated @ 0hr, biological rep1


title: wild-type_20h_syn2

status: Public on Aug 03 2008

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

source_name: T. thermophilus HB8, wild-type, synthetic midium, 20 hrs

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

growth_protocol:
T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of synthetic medium. The cells (2 ml) were inoculated into 500 ml of the same medium and then cultivated at 70°C for 20 h (OD600nm = ~ 4.6).
The synthetic medium was made by mixing 500 ml of solutions A (4% sucrose) and B, 5 ml of solution C, 1 ml of solution D and 0.1 ml of each metal solution. Solution B was composed of 4% sodium glutamate, 0.11% K2HPO4, 0.036% KH2PO4, 0.4% NaCl and 0.1% (NH4)2SO4, which was adjusted to pH 7.3 with 3 M NaOH. Solution C was composed of 2.5% MgCl2·6H2O and 0.5% CaCl2·2H2O. Solution D was composed of 1% biotin and 10% thiamine. The matal solutions were as follows: 10% FeSO4·7H2O, 1.2% Na2MoO4·2H2O, 0.1% VOSO4·xH2O, 0.5% MnCl2·4H2O, 0.06% ZnSO4·7H2O, 0.015% CuSO4·5H2O, 0.8% CoCl2·6H2O and 0.02% NiCl2·6H2O.

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.

tag: wild-type T. thermophilus HB8 strain grown on a synthetic medium for 20 hours (stationary-phase).


title: wild-type_20h_syn1


title: wild-type_10h_syn3

source_name: T. thermophilus HB8, wild-type, synthetic midium, 10 hrs

growth_protocol:
T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of synthetic medium. The cells (2 ml) were inoculated into 500 ml of the same medium and then cultivated at 70°C for 10 h (OD600nm = ~ 0.5).
The synthetic medium was made by mixing 500 ml of solutions A (4% sucrose) and B, 5 ml of solution C, 1 ml of solution D and 0.1 ml of each metal solution. Solution B was composed of 4% sodium glutamate, 0.11% K2HPO4, 0.036% KH2PO4, 0.4% NaCl and 0.1% (NH4)2SO4, which was adjusted to pH 7.3 with 3 M NaOH. Solution C was composed of 2.5% MgCl2·6H2O and 0.5% CaCl2·2H2O. Solution D was composed of 1% biotin and 10% thiamine. The matal solutions were as follows: 10% FeSO4·7H2O, 1.2% Na2MoO4·2H2O, 0.1% VOSO4·xH2O, 0.5% MnCl2·4H2O, 0.06% ZnSO4·7H2O, 0.015% CuSO4·5H2O, 0.8% CoCl2·6H2O and 0.02% NiCl2·6H2O.

tag: wild-type T. thermophilus HB8 strain grown on a synthetic medium for 10 hours (log-phase).


title: wild-type_10h_syn2


title: wild-type_10h_syn1


title: T 2

description: microRNA expression

source_name: T 2


title: Nipponbare_young panicle 2cm, biological rep2

status: Public on Jun 09 2009

city: Mishima

first: Nori

last: Kurata

address: 1111 Yata

institute: National Institute of Genetics

description: Gene expression data from rice young panicle

hyb_protocol: According to Affymetrix standard procedure, 10 micrograms of fragmented cRNA were hybridized to an array for 16-18 hours at 45°C with constant rotation at 60 rpm. After hybridization, the array was washed and stained using an Affymetrix Fluidics Station.

scan_protocol: GeneChips were scanned using Affymetrix GeneArray 3000 scanner.

data_processing: The data were analyzed with GCOS 1.3 using Affymetrix default analysis settings and global scaling as normalization method.

organism: Oryza sativa Japonica Group

source_name: young panicle 2cm

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: total RNA was isolated and purified by RNeasy Plant Mini Kit (QIAGEN)

value: young panicle

tag: cultivar

value: Nipponbare


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

description: wild-type strain ϕYS40 pre-infection 2

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

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 (OD600nm = ~ 0.87).

value: wild-type

tag: protocol

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


title: TTHA1359 deletion mutant strain 680_2

description: TTHA1359 deletion mutant strain 680_2

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

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

growth_protocol: The T. thermophilus HB8 TTHA1359 deletion mutant strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 680 min (OD600nm = ~ 5.5).

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

tag: TTHA1359 deletion mutant strain grown on a rich (TR) medium for 680 min


title: control -dox repl.2

status: Public on Oct 20 2008

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

address: Ctra. Can Ruti, Camí de les escoles s/n

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

description: Negative control for transfection, biological replicate 2 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and empty shRNA expression vector (pLVTHM) uninduced

hyb_protocol: For each sample, 750 ng of biotinylated cRNA were hybridized in a BeadChip Hyb Chamber with rocking 16 h at 58ºC. The day after the bead arrays were washed with Illumina proprietary washing solutions in a Hybex waterbath: first with static incubation for 10 min at 55ºC in E1BC solution, followed by 10 rinses by dipping in the same solution and shaking 5 min at 90 rpm in an orbital shaker; the next wash was by dipping 10 times in 100% ethanol and shaking 10 min at 110 rpm in an orbital shaker; this was followed by another wash in E1BC solution with 10 dippings followed by 2 min shaking at 90 rpm. Washed bead arrays were blocked in E1 buffer 10 min in rocking incubator and 10 additional minutes with 2 ml of E1 buffer plus streptavidin-Cy3. The fluorescent reagent was washed away with E1BC solution with 10 dippings plus 5 min shaking at 140 rpm. Finally beadarrays were dried by centrifugation 4 min at 275 rcf, followed by scanning in a Illumina Beadstation.

scan_protocol: The Beadscan software was used to control de scanner, generate .tif images and extract the raw data as tabulated text files. Default settings for DirectHyb Gene Expression were used.

data_processing: The raw data was summarized per probe using BeadStudio software Gene Expression module and the summary data file was processed using the PILLA web einterface tool (Lozano et al, unpublished), an implementation of the Lumi package (Du et al, 2008) developed within the Bioconductor project in the R statistical programming environment (Gentleman et al, 2004). Data were normalized using the rsn method and vst as the variance stabilization method. The log2 intensities were median centered and log ratios were computed as differences in log2 intensities for each probe. The SAM  (significance analysis of microarrays) two class unpaired comparison test was applied with 100 permutations to detect statistically significant differences in gene expression between treated and control conditions (Tusher et al, 2001).

label: biotin / streptavidin-Cy3

source_name: empty shRNA vector; uninduced, no doxycyclin treatment

label_protocol: For each sample 200 ng of total RNA were reverse transcribed, amplified by in vitro transcription and labelled with biotin-UTP using the Illumina Total Prep RNA amplification kit (IL1791, Ambion) following the manufacturer's instructions. Labelled sample quality was assessed by spectrophotometry and bioanalyzer. After preheating at 65ºC for 5 min.

growth_protocol: Cell lines were grown in RPMI 1640 medium, supplemented with 10% FBS, 2mM L-glutamine, 100 U/ml penicillin, and 100µg/ml streptomycin.

extract_protocol: Total RNA was extracted using the RNAsy Kit (Qiagen). RNA concentration was measured with a small volume spectrophotometer (Nanodrop). The quality of the RNA was analyzed using the Agilent Bioanalyzer 2100 and the RNA 6000 LabChip Kit (Agilent) with the Eukaryote Total RNA Nano Assay, with RIN ranging between 9.2 and 9.8.

treatment_protocol: Plasmids for the lentivirus vector-mediated drug-inducible RNA interference system (pLVTHM, ptTR-KRAB-Red, pCMC-R8.91 and pMD.G) were provided by D. Trono (University of Geneva). The 64-mer oligonucleotides for histone H1 shRNA cloning into MluI/ClaI-digested pLVTHM were designed, annealed and phosphorylated as communicated by D. Trono (http://tronolab.epfl.ch/). Oligonucleotides have the following general structure: 5'-CGCGTCCCC-N19 TTCAAGAGA-rcN19-TTTTTGGAAAT-3' and 5'-AGGGG-N19-AAGTTCTCT-rcN19-AAAAACCTTTAGC-3', being N19 the specific target sequence for each H1 variant and rcN19 its reverse complementary sequence. The corresponding 19-mer gene-specific target sequences for interference were designed manually following standard rules (AAN19, GC % 30-70). Target sequences (N19) are CGCTGACTCGCAGATCAAG for H1.0, AGAGCGTAGCGGAGTTTCT for H1.2, CTGCCAAGAGTCCAGCTAA for H1.3, GAAGAGCGCCAAGAAGACC for H1.4 and GGCAACTAAGAAGGCTGCC for H1.5.  For the production of viral particles containing the HIV-derived vectors, 2.5x106 HEK 293T cells (Clontech) were transfected with plasmids ptTR-KRAB-Red, pLVTHM-shH1.n or pEV833-HA-H1.n (10µg), pCMV-R8.91 (6.5µg) and pMD.G (3.5µg) in 10 cm dishes using calcium phosphate. Medium was collected every 24 hours for 2 days and centrifuged 1h30min at 26.000 rpm at 4ºC in a sucrose gradient to concentrate viruses. Pellet containing viral particles was dissolved in medium and used for cell infection. Cells were infected using the spinoculation method, i.e. plates were centrifuged at 1,200 x g for 2 hr at 25 ºC.  Initially, a cell line expressing the Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) was generated. Then, this cell line was infected with viruses for expression of the different H1 variants shRNAs (pLVTHM). The inducible knocked-down cell lines were sorted in a FACSvantageSE (Becton Dickinson) for RedFP-positive and GFP-positive fluorescence after 3 days of Dox treatment. Then cells were amplified in the absence of Dox until an experiment was performed. Doxicycline (Sigma) was added at 2.5 µg/ml when indicated. Along a 6-day treatment with Dox, cells were passaged at day 3. Serum-containing media was replaced with serum-free media at day 4 for growth arrest.

tag: T47D-MTVL (breast cancer cell line carrying one stably integrated copy of luciferase reporter gene driven by the MMTV promoter) stably infected with an inducible system for the expression of shRNAs.Cells stably express RedFP and KRAB repressor fused to Tet regulator.Upon Dox treatment, cells express RedFP and the cloned shRNA.

tag: no depletion

tag: empty shRNA vector

tag: uninduced, no doxycyclin treatment


title: TTHA1359 deletion mutant strain 680_1

description: TTHA1359 deletion mutant strain 680_1

growth_protocol: The T. thermophilus HB8 TTHA1359 deletion mutant strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 680 min (OD600nm = ~ 3.6).


title: wild-type strain 680_4

description: wild-type strain 680_4

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 TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 680 min (OD600nm = ~ 4.2).

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 680 min


title: wild-type strain 760_3

description: wild-type strain 760_3

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 TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 760 min (OD600nm = ~ 6.9).

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 760 min


title: TTHA1359 deletion mutant strain 680_3

description: TTHA1359 deletion mutant strain 680_3

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: wild-type strain 480_3

description: wild-type strain 480_3

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 TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 480 min (OD600nm = ~ 4.0).

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 480 min


title: wild-type strain 360_3

description: wild-type strain 360_3

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 TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 360 min (OD600nm = ~ 0.98).

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 360 min


title: wild-type strain 680_3

description: wild-type strain 680_3

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 680 min (OD600nm = ~ 6.6).


title: wild-type strain 180_3

description: wild-type strain 180_3

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

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 180 min (OD600nm = ~ 0.06).

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

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


title: TTHA1359 deletion mutant strain 680_4

description: TTHA1359 deletion mutant strain 680_4

growth_protocol: The T. thermophilus HB8 TTHA1359 deletion mutant strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 680 min (OD600nm = ~ 3.5).


title: wild-type strain 600_3

description: wild-type strain 600_3

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 TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 600 min (OD600nm = ~ 5.8).

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 600 min


title: control -dox repl.1

description: Negative control for transfection, biological replicate 1 of 2; T47D-MTVL cells transfected with Dox-responsive KRAB repressor and RedFP (ptTR-KRAB-Red) and empty shRNA expression vector (pLVTHM) uninduced


title: wild-type_20h_syn3


title: wild-type strain 420_3

description: wild-type strain 420_3

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

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 420 min (OD600nm = ~ 2.7).

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

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 420 min


title: wild-type strain 240_3

description: wild-type strain 240_3

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 TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 240 min (OD600nm = ~ 0.15).

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 240 min


title: wild-type strain 540_2

description: wild-type strain 540_2

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 TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 540 min (OD600nm = ~ 4.5).

tag: wild-type Thermus thermophilus HB8 strain grown on a rich (TR) medium for 540 min


title: wild-type strain 540_3

description: wild-type strain 540_3

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 540 min (OD600nm = ~ 4.7).


title: wild-type strain 600_2

description: wild-type strain 600_2

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 600 min (OD600nm = ~ 5.2).


title: wild-type strain 680_2

description: wild-type strain 680_2

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 680 min (OD600nm = ~ 5.9).


title: wild-type strain 480_2

description: wild-type strain 480_2

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 480 min (OD600nm = ~ 4.3).


title: wild-type strain 420_1

description: wild-type strain 420_1

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 420 min (OD600nm = ~ 2.0).


title: wild-type strain 360_2

description: wild-type strain 360_2

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 360 min (OD600nm = ~ 1.2).

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.


title: wild-type strain 480_1

description: wild-type strain 480_1

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 480 min (OD600nm = ~ 3.0).


title: wild-type strain 420_2

description: wild-type strain 420_2

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 420 min (OD600nm = ~ 3.0).


title: wild-type strain 540_1

description: wild-type strain 540_1

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 540 min (OD600nm = ~ 3.9).


title: wild-type strain 600_1

description: wild-type strain 600_1

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 600 min (OD600nm = ~ 4.5).


title: wild-type strain 240_2

description: wild-type strain 240_2

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 240 min (OD600nm = ~ 0.17).


title: wild-type strain 180_2

description: wild-type strain 180_2

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 180 min (OD600nm = ~ 0.06).


title: wild-type strain 760_1

description: wild-type strain 760_1

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 760 min (OD600nm = ~ 5.5).


title: wild-type strain 300_2

status: Public on Jul 16 2008

description: wild-type strain 300_2

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

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 300 min (OD600nm = ~ 0.45).

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

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


title: wild-type strain 240_1

description: wild-type strain 240_1

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 240 min (OD600nm = ~ 0.13).


title: wild-type strain 760_2

description: wild-type strain 760_2

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 760 min (OD600nm = ~ 7.3).


title: wild-type strain 300_3

description: wild-type strain 300_3

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 300 min (OD600nm = ~ 0.35).


title: wild-type strain 360_1

description: wild-type strain 360_1

growth_protocol: The T. thermophilus HB8 wild-type strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 360 min (OD600nm = ~ 0.73).


title: TTHB212 deletion mutant strain 2

description: TTHB212 deletion mutant strain 2

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

growth_protocol: The T. thermophilus HB8 TTHB212 deletion mutant strain was pre-cultured at 70°C for 16 h in 3 ml of TR medium containing 0.8% polypeptone, 0.4% yeast extract, 0.2% NaCl, 0.4 mM CaCl2, and 0.4 mM MgCl2, which was adjusted to pH 7.2 with NaOH. The cells (2 ml) were inoculated into 1 liter of the same medium and then cultivated at 70°C for 7 h (OD600nm = ~ 0.44).

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