Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Fob3b vs F-line

ABSTRACT: Liver and BAT expression differences between the fat F-line, and congenic Fob3b-line. Normalised data appended as follows: TABLE 1: LIVER - 1st set (7.5K) of the 2 slide NIA NIH 15K set -source1 = F-line liver male - 2 pools each made from 5 different individuals -source2 = Fob3b-line (aka Fchr15D-line) liver male - 2 pools each made from 5 different individuals -values are normalised using mixed model across 6 slides: 1 F-line vs Fline 2 Fob3b-line vs Fob3b-line 3 F-line pool1 vs Fob3b-line pool1 4 F-line pool1 vs Fob3b-line pool1 -dye swap 5 F-line pool2 vs Fob3b-line pool2 6 F-line pool2 vs Fob3b-line pool2 -dye swap TABLE 2: LIVER - 2nd set (7.5K) of the 2 slide NIA NIH 15K set -source1 = F-line liver male - 2 pools each made from 5 differnt individuals -source2 = Fob3b-line (aka Fchr15D-line) liver male - 2 pools each made from 5 differnt individuals -values are normalised using mixed model across 6 slides: 1 F-line Vs F-line 2 Fob3b-line vs Fob3b-line 3 F-line pool1 vs Fob3b-line pool2 4 F-line pool1 vs Fob3b-line pool2 dye swap 5 F-line pool2 vs Fob3b-line pool1 6 F-line pool2 vs Fob3b-line pool1 dye swap TABLE 3: Brown Adipose Tissue (BAT) 1st (7.5K) array set of 15K NIA NIH set -source1 = F-line male BAT from 2 pools each made from 5 different individuals -source2 = Fob3b-line (aka Fchr15D-line) male BAT from 2 pools each made from 5 different individuals -values are normalised using mixed model across 4 slides: 1 F-line pool1 vs Fob3b-line pool1 2 F-line pool1 vs Fob3b-line pool1 dye swap 3 F-line pool2 vs Fob3b-line pool2 4 F-line pool2 vs Fob3b-line pool2 dye swap TABLE 4: Brown Adipose Tissue (BAT) 2nd (7.5K) array of the 15K NIA NIH set -source1 = F-line male BAT (2 pools each from 5 individual mice) -source2 = Fob3b-line (aka Fchr15D-line) male BAT (2 pools each from 5 individual mice) -values are normalised using mixed model across 4 slides: 1 F-line pool1 vs Fob3b-line pool1 2 F-line pool1 vs Fob3b-line pool1 dye swap 3 F-line pool2 vs Fob3b-line pool2 4 F-line pool2 vs Fob3b-line pool2 dye swap Keywords = Obesity Keywords = Fob3b Keywords = QTL Keywords = congenic

ORGANISM(S): Mus musculus

SUBMITTER: Michael Clinton

PROVIDER: E-GEOD-1558 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Microarray gene expression analysis of the Fob3b obesity QTL identifies positional candidate gene Sqle and perturbed cholesterol and glycolysis pathways.

Stylianou Ioannis M IM Clinton Michael M Keightley Peter D PD Pritchard Clare C Tymowska-Lalanne Zuzzana Z Bünger Lutz L Horvat Simon S

Physiological genomics 20041214 3

Obesity-related diseases are poised to become the primary cause of death in developed nations. While a number of monogenic causes of obesity have recently been identified, these are responsible for only a small proportion of human cases of obesity. Quantitative trait locus (QTL) studies using animal models have revealed hundreds of potential loci that affect obesity; however, few have been further analyzed beyond the original QTL scan. We previously mapped four QTL in an F(2) between divergently ...[more]

PMID: 15598878

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Project description:Batch cultures of Wild-type C. jejuni NCTC11168 were grown in 150 ml volumes of Mueller-Hinton broth in 250 ml baffled flasks. Microaerophilic conditions were generated using a MACS-VA500 microaerophilic work station (10 % O2, 10 % CO2, 80 % N2) from Don Whitley Scientific, Ltd which also maintained the growth temperature at 42 ÂºC. When mid-exponential phase was reached 0.25 mM GSNO was added to half of the cultures. After a 10 minute exposure samples of both treated and untreated cells were harvested into phenol/ethenol to stabilize the RNA and total RNA was purified using Qiagenâs RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis. A C. jejuni cgb mutant was grown in two parallel custom-built chemostats based on Sigma Proculture Dynalift spinner flasks with a working volume of 125 ml, and the dilution rate (which at steady state is equal to the specific growth rate) of 0.1 h-1. A gas mix of 10% O2, 10% CO2 and 80% N2 was passed into the head space of the culture vessel at a rate of 0.25 l min-1 to obtain a microaerobic atmosphere, and silicone water jackets maintained the temperature at 42 ÂºC. The flasks were placed on KMO 2 basic IKA-Werke stirrers (arbitrary setting, 260; Scientific Laboratory Supplies), which gaveeffective transfer of O2 from the gaseous atmosphere to the culture by virtue of a stable vortex. A fresh overflow sample was used to check the pH at the time of harvest (which was consistently between 6.6 and 7) and to ensure that there was no contamination by plating a 20 Î¼l sample onto both nutrient agar plates incubated at 37 Â°C at atmospheric oxygen, and Mueller-Hinton plates incubated at 42 Â°C in the microaerophilic work station. When staedy-state was reached, as verified by collecting at least 5 culture volumes, GSNO (final concentration 0.25 mM) was added to one culture. After a further 10 min the 125 ml volume was separated into 3 equal volumes and each was mixed immediately on ice with 3.56 ml 100% ethanol and 185 ml phenol to stabilize the RNA. The cells were subsequently harvested by centrifugation. Total RNA was purified by using a Qiagen RNeasy Mini kit as recommended by the supplier. cDNA synthesis was carried out using 12 Âµg of starting material, which was primed with 9 Âµg of pd(N)6 random hexamers (Amersham Biosciences). Reaction mixtures (20 Âµl) containing 0.5 mM ATP, 0.5 mM TTP, 0.5 mM GTP, 0.2 mM CTP, and 1 mM Cy3- or 1 mM Cy5-dCTP were incubated for 2 h at 42 Â°C with 200 U of Superscript II RNase H reverse transcriptase (Invitrogen). Following synthesis, cDNA was purified by using a PCR purification kit (Qiagen) to remove the unincorporated deoxynucloside triphosphates, fluorescent dye, and primers. Equal volumes of cDNA were combined and evaporated to near dryness with an SPD121P Speed Vac (Thermon Savant). For hybridisation to the microarray slides, cDNA was resuspended in an appropriate volume of salt-based hybridization buffer (provided by Ocimum Biosolutions). Prior to addition to the slides, cDNA samples were heated to 95 Â°C for 3 min, and then placed on ice for no more than 3 min. The slides were placed in MWG Biotech hybridization chambers and incubated for 16 to 24 h in a shaking water bath at 110 rpm and 42 Â°C. Following incubation , the slides were washed sequentially for 5 min in 2x SSC-1 % sodium dodecyl sulphate, 1x SSC, 0.5x SSC and 0.1x SSC at 37 Â°C with gentle agitation (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate). The slides were dried by centrifugation at 254 xg for 5 min and subsequently scanned with an Affymetrix 428 scanner. The average signal intensity and local background correction were obtained by using commercially available software from Biodiscovery, Inc. (Imagine version 4.0, and Genesight, version 3.5). The mean values from each channel were log2 transformed and normalized by using the subtract-by-mean method to remove intensity-dependent effects in the log2 (ratio) values. The Cy3/Cy5 fluorescence ratios were calculated from the normalized values. Biological experiments (i.e. chemostat growth with and without 0.25 mM GSNO addition) were carried out three times and a dye swap was performed for two of the three experiments which provided two technical repeats, one each for two of the three biological repeats. Data from the independent experiments were combined. Genes that were differentially expressed â¥ twofold and displayed and P value of â¤ 0.05 (as determined by a t test) were defined as being statistically significantly differentially transcribed.

Project description:Wild-type Campylobacter jejuni NCTC11168 was grown in 2 homemade, parallel chemostats. Cells were grown in 125 ml volumes of Mueller-Hinton Broth where the growth rate was controlled by the dilution rate (0.1 h-1). A gas mix of 80% nitrogen, 10% carbon dioxide and 10% oxygen was pumped into the head-space of the vessels at a rate of 0.25 l/min to obtain a microaerobic environment and the culture was maintained at 42 ÂºC via a water jacket. Cells were grown as above until steady-state had been reached. At steady-state one of the cultures was exposed to 10 uM NOC-5 & -7 (final concentration) for a period of 10 min. Samples of both the control and stressed cultures were harvested into phenol/ethanol to stabilize the RNA and total RNA was purified using Qiagenâ??s RNeasy Mini kit (as recommended by the suppliers) prior to use in microarray analysis. Equal quantities of RNA from control and GSNO-supplemented cultures were labelled using nucleotide analogues of dCTP containing either Cy3 or Cy5 fluorescent dyes. The average signal intensity and local background correction were obtained using a commercially available software package from Biodiscovery, Inc (Imagene, version 4.0 and GeneSight, version 4). The mean values from each channel were log2 transformed and normalised using the Lowess method to remove intensity-dependent effects in the log2(ratios) values. The Cy3/Cy5 fluorescent ratios were calculated from the normalized values. C. jejuni NCTC11168 was grown in two parallel custom-built chemostats based on Sigma Proculture Dynalift spinner flasks with a working volume of 125 ml, and the dilution rate (which at steady state is equal to the specific growth rate) of 0.1 h-1. A gas mix of 10% O2, 10% CO2 and 80% N2 was passed into the head space of the culture vessel at a rate of 0.25 l min-1 to obtain a microaerobic atmosphere, and silicone water jackets maintained the temperature at 42 ÂºC. The flasks were placed on KMO 2 basic IKA-Werke stirrers (arbitrary setting, 260; Scientific Laboratory Supplies), which gaveeffective transfer of O2 from the gaseous atmosphere to the culture by virtue of a stable vortex. A fresh overflow sample was used to check the pH at the time of harvest (which was consistently between 6.6 and 7) and to ensure that there was no contamination by plating a 20 Î¼l sample onto both nutrient agar plates incubated at 37 Â°C at atmospheric oxygen, and Mueller-Hinton plates incubated at 42 Â°C in the microaerophilic work station. When staedy-state was reached, as verified by collecting at least 5 culture volumes, NOC-5 & -7 (final concentration 10 uM) was added to one culture. After a further 10 min the 125 ml volume was separated into 3 equal volumes and each was mixed immediately on ice with 3.56 ml 100% ethanol and 185 ml phenol to stabilize the RNA. The cells were subsequently harvested by centrifugation. Total RNA was purified by using a Qiagen RNeasy Mini kit as recommended by the supplier. cDNA synthesis was carried out using 12 Âµg of starting material, which was primed with 9 Âµg of pd(N)6 random hexamers (Amersham Biosciences). Reaction mixtures (20 Âµl) containing 0.5 mM ATP, 0.5 mM TTP, 0.5 mM GTP, 0.2 mM CTP, and 1 mM Cy3- or 1 mM Cy5-dCTP were incubated for 2 h at 42 Â°C with 200 U of Superscript II RNase H reverse transcriptase (Invitrogen). Following synthesis, cDNA was purified by using a PCR purification kit (Qiagen) to remove the unincorporated deoxynucloside triphosphates, fluorescent dye, and primers. Equal volumes of cDNA were combined and evaporated to near dryness with an SPD121P Speed Vac (Thermon Savant). For hybridisation to the microarray slides, cDNA was resuspended in an appropriate volume of salt-based hybridization buffer (provided by Ocimum Biosolutions). Prior to addition to the slides, cDNA samples were heated to 95 Â°C for 3 min, and then placed on ice for no more than 3 min. The slides were placed in MWG Biotech hybridization chambers and incubated for 16 to 24 h in a shaking water bath at 110 rpm and 42 Â°C. Following incubation , the slides were washed sequentially for 5 min in 2x SSC-1 % sodium dodecyl sulphate, 1x SSC, 0.5x SSC and 0.1x SSC at 37 Â°C with gentle agitation (1x SSC is 0.15 M NaCl plus 0.015 M sodium citrate). The slides were dried by centrifugation at 254 xg for 5 min and subsequently scanned with an Affymetrix 428 scanner. The average signal intensity and local background correction were obtained by using commercially available software from Biodiscovery, Inc. (Imagine version 4.0, and Genesight, version 3.5). The mean values from each channel were log2 transformed and normalized by using the subtract-by-mean method to remove intensity-dependent effects in the log2 (ratio) values. The Cy3/Cy5 fluorescence ratios were calculated from the normalized values. Biological experiments (i.e. chemostat growth with and without 0.25 mM GSNO addition) were carried out three times and a dye swap was performed for two of the three experiments which provided two technical repeats, one each for two of the three biological repeats. Data from the independent experiments were combined. Genes that were differentially expressed â?¥ twofold and displayed and P value of â?¤ 0.05 (as determined by a t test) were defined as being statistically significantly differentially transcribed.

Dataset Information

Fob3b vs F-line

Publications

Microarray gene expression analysis of the Fob3b obesity QTL identifies positional candidate gene Sqle and perturbed cholesterol and glycolysis pathways.

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