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Search results for the GEO ID: GSE11125

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GSM280631

GPL339

Liver_repeated stress_bio rep 1_tech rep 1

Liver, repeated stress, bio rep 1, tech rep 1

strain: BALB/c gender: female age: 10 to 12 weeks Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation

Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.

Sample_geo_accession	GSM280631
Sample_status	Public on Jun 01 2008
Sample_submission_date	Apr 10 2008
Sample_last_update_date	May 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.
Sample_growth_protocol_ch1	Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.
Sample_hyb_protocol	For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.
Sample_platform_id	GPL339
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280631/suppl/GSM280631.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280631/suppl/GSM280631.CHP.gz
Sample_series_id	GSE11125
Sample_series_id	GSE11126
Sample_data_row_count	22690

GSM280632

GPL339

Liver_repeated stress_bio rep 1_tech rep 2

Liver, repeated stress, bio rep 1, tech rep 2

strain: BALB/c gender: female age: 10 to 12 weeks Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation

Sample_geo_accession	GSM280632
Sample_status	Public on Jun 01 2008
Sample_submission_date	Apr 10 2008
Sample_last_update_date	May 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.
Sample_growth_protocol_ch1	Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.
Sample_hyb_protocol	For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.
Sample_platform_id	GPL339
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280632/suppl/GSM280632.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280632/suppl/GSM280632.CHP.gz
Sample_series_id	GSE11125
Sample_series_id	GSE11126
Sample_data_row_count	22690

GSM280633

GPL339

Liver_repeated stress_bio rep 2_tech rep 1

Liver, repeated stress, bio rep 2, tech rep 1

strain: BALB/c gender: female age: 10 to 12 weeks Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation

Sample_geo_accession	GSM280633
Sample_status	Public on Jun 01 2008
Sample_submission_date	Apr 10 2008
Sample_last_update_date	May 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.
Sample_growth_protocol_ch1	Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.
Sample_hyb_protocol	For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.
Sample_platform_id	GPL339
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280633/suppl/GSM280633.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280633/suppl/GSM280633.CHP.gz
Sample_series_id	GSE11125
Sample_series_id	GSE11126
Sample_data_row_count	22690

GSM280634

GPL339

Liver_repeated stress_bio rep 2_tech rep 2

Liver, repeated stress, bio rep 2, tech rep 2

strain: BALB/c gender: female age: 10 to 12 weeks Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation

Sample_geo_accession	GSM280634
Sample_status	Public on Jun 01 2008
Sample_submission_date	Apr 10 2008
Sample_last_update_date	May 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.
Sample_growth_protocol_ch1	Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.
Sample_hyb_protocol	For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.
Sample_platform_id	GPL339
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280634/suppl/GSM280634.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280634/suppl/GSM280634.CHP.gz
Sample_series_id	GSE11125
Sample_series_id	GSE11126
Sample_data_row_count	22690

GSM280635

GPL339

Liver_control for repeated stress_bio rep 1_tech rep 1

Liver, control for repeated stress, bio rep 1, tech rep 1

strain: BALB/c gender: female age: 10 to 12 weeks Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation

Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. All successive experiments and analyses were performed starting at 1000 a.m. on the 5th day.

Sample_geo_accession	GSM280635
Sample_status	Public on Jun 01 2008
Sample_submission_date	Apr 10 2008
Sample_last_update_date	May 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.
Sample_growth_protocol_ch1	Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.
Sample_hyb_protocol	For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.
Sample_platform_id	GPL339
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280635/suppl/GSM280635.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280635/suppl/GSM280635.CHP.gz
Sample_series_id	GSE11125
Sample_series_id	GSE11126
Sample_data_row_count	22690

GSM280636

GPL339

Liver_control for repeated stress_bio rep 1_tech rep 2

Liver, control for repeated stress, bio rep 1, tech rep 2

strain: BALB/c gender: female age: 10 to 12 weeks Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation

Sample_geo_accession	GSM280636
Sample_status	Public on Jun 01 2008
Sample_submission_date	Apr 10 2008
Sample_last_update_date	May 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.
Sample_growth_protocol_ch1	Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.
Sample_hyb_protocol	For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.
Sample_platform_id	GPL339
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280636/suppl/GSM280636.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280636/suppl/GSM280636.CHP.gz
Sample_series_id	GSE11125
Sample_series_id	GSE11126
Sample_data_row_count	22690

GSM280637

GPL339

Liver_control for repeated stress_bio rep 2_tech rep 1

Liver, control for repeated stress, bio rep 2, tech rep 1

strain: BALB/c gender: female age: 10 to 12 weeks Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation

Sample_geo_accession	GSM280637
Sample_status	Public on Jun 01 2008
Sample_submission_date	Apr 10 2008
Sample_last_update_date	May 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.
Sample_growth_protocol_ch1	Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.
Sample_hyb_protocol	For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.
Sample_platform_id	GPL339
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280637/suppl/GSM280637.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280637/suppl/GSM280637.CHP.gz
Sample_series_id	GSE11125
Sample_series_id	GSE11126
Sample_data_row_count	22690

GSM280638

GPL339

Liver_control for repeated stress_bio rep 2_tech rep 2

Liver, control for repeated stress, bio rep 2, tech rep 2

strain: BALB/c gender: female age: 10 to 12 weeks Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation

Sample_geo_accession	GSM280638
Sample_status	Public on Jun 01 2008
Sample_submission_date	Apr 10 2008
Sample_last_update_date	May 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_treatment_protocol_ch1	Mice were exposed to combined acoustic and restraint stress on four successive days, for 2 h twice a day during the physiological recovery phase of rodents (0800-1000 a.m. and 0400-0600 p.m.). On day 5 only one stress session was performed in the morning. For immobilization mice were placed in 50-ml conical centrifuge tubes with multiple ventilation holes without penning the tail. Acoustic stress was induced by a randomized ultrasound emission device between 19 and 25 kHz with 0-35 dB waves in attacks (SiXiS; Pat.NO.109977, Taiwan) allowing the mice no adaptation to the stressor (8, 14). Between the stress sessions mice stayed in their home cages and had free access to food and tap water. Control mice were kept isolated from stressed animals during the 4.5 days of stress exposure to avoid any acoustic or olfactory communication between the groups. Therefore, the non-stressed group stayed in the incubator where the animals were adapted. The stressed mice remained outside the incubator in the same animal laboratory during the whole period of the stress model. All successive experiments and analyses were performed starting at 1000 a.m. after the ninth stress exposure.
Sample_growth_protocol_ch1	Female BALB/c mice aged 6-8 weeks were randomly grouped into the experimental and control groups starting at least 4 weeks before being used in experiments. The group size in different experiments differed from 6-12 mice per cage. Animals stayed in their group until the end of the experiments and were not mixed up to avoid social stress. All animals were maintained with sterilized food (ssniff R-Z, ssniff Spezialdiäten GmbH, Soest, Germany) and tap water ad libitum for adaptation under minimal stress conditions. Animal rooms were on 12:12 light/dark cycle and were maintained at a constant environment prior to the experiment. In order to avoid any additional effect (for example acoustic or olfactory effects) the handling of mice during the adaptation period and during the experiments was restricted to one investigator. All animal procedures were carried out as approved by the Ethics Committee for Animal Care of Mecklenburg-Vorpommern, Germany.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Organs of unnarcotized mice were explanted immediately after cervical dislocation in order to avoid RNA degradation. For liver samples a small piece of tissue was immediately homogenized with a micropestle in 350 µl Buffer RLT/ 1% β-Mercapoethanol (QIAGEN GmbH, Hilden, Germany/Sigma-Aldrich Chemie GmbH, München, Germany). The liver lysates were shock frozen in liquid nitrogen. All samples were stored at -70°C. Liver sample lysates were thawed and processed at room temperature for RNA preparation with a RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany) according to the manufacturer’s instructions. After ethanol precipitation the RNA was quantified spectrophotometrically and its quality was verified using an Agilent 2100 Bioanalyzer and RNA Nano Chips (Agilent Technologies Inc., Santa Clara, CA, USA).
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Synthesis of labeled material for hybridization started with reverse transcription of 5 µg of total RNA of sample pools and was followed by the synthesis of the second DNA strand according to the manufacturer’s protocols. Reaction products were deproteinized with phenol, chloroform and isoamylalcohol using Phase-Lock-Gel Tubes Light (Eppendorf AG, Hamburg, Germany). DNA was precipitated with 0.5 vol. 7.5 M ammoniumacetate and 2.5 vol. prechilled ethanol and resuspended in 11 µl of water. 10 µl of double-stranded cDNA solution served as template for an in-vitro-transcription reaction (IVT) using GeneChip Expression 3’ Amplification Reagents (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s instructions. The resulting labeled cRNA products were cleaned up with the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany). Concentration and quality of cRNA were measured with a photometer and an Agilent 2100 Bioanalyzer, respectively. The samples were stored at -20°C until the hybridization.
Sample_hyb_protocol	For hybridization 12.5 µg of cRNA were fragmented in 1x fragmentation buffer according the the manufacturer’s instructions, added to the hybridization cocktail with final concentrations of 0.05 nM B2 Oligo, 1x hybridization controls, 0.094 mg/ml Salmon Testes DNA and 0.5 mg/ml acetylated BSA in 1x hybridization buffer and denatured. After prehybridization Affymetrix GeneChip Mouse Expression Arrays 430A were loaded with 200 µl hybridization cocktail and hybridized 16 h at 45°C with rotation at 60 rpm.
Sample_scan_protocol	Arrays were washed and stained using the GeneChip FluidicsStation 400 (Affymetrix, Santa Clara, CA, USA) according to the manufacturer’s protocol and scanned using the Agilent GeneArray Scanner (Agilent Technologies Inc., Santa Clara, CA, USA) under the control of Microarray Analysis Suite (MAS) 5.0 software (Affymetrix, Santa Clara, CA, USA).
Sample_data_processing	EXP-, DAT-, CEL-files were transferred to GeneChip Operating Software (GCOS) 1.2 (Affymetrix, Santa Clara, CA, USA). CHP-files were generated with standard expression analysis settings (MAS algorithm) using the scaling procedure and a target value of 150.
Sample_platform_id	GPL339
Sample_contact_name	Maren,,Depke
Sample_contact_department	Department of Functional Genomics
Sample_contact_institute	Ernst-Moritz-Arndt-University Greifswald, Interfaculty Institute of Genetics and Functional Genomics
Sample_contact_address	F.-L.-Jahn-Str. 15a
Sample_contact_city	Greifswald
Sample_contact_zip/postal_code	17489
Sample_contact_country	Germany
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280638/suppl/GSM280638.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM280nnn/GSM280638/suppl/GSM280638.CHP.gz
Sample_series_id	GSE11125
Sample_series_id	GSE11126
Sample_data_row_count	22690

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