Search results for the GEO ID: GSE20344  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM509688 | GPL1355 |
|
BLA_sucrose_rep 1
|
BLA tissue after 14 days, 2x daily limited sucrose
|
treatment protocol: 30% sucrose snack treatment
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Sucrose-BLA pooled from rats 1 and 7
|
| Sample_geo_accession | GSM509688
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509688/suppl/GSM509688.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509689 | GPL1355 |
|
BLA_sucrose_rep 2
|
BLA tissue after 14 days, 2x daily limited sucrose
|
treatment protocol: 30% sucrose snack treatment
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Sucrose-BLA pooled from rats 2 and 8
|
| Sample_geo_accession | GSM509689
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509689/suppl/GSM509689.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509690 | GPL1355 |
|
BLA_sucrose_rep 3
|
BLA tissue after 14 days, 2x daily limited sucrose
|
treatment protocol: 30% sucrose snack treatment
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Sucrose-BLA pooled from rats 3 and 9
|
| Sample_geo_accession | GSM509690
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509690/suppl/GSM509690.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509691 | GPL1355 |
|
BLA_sucrose_rep 4
|
BLA tissue after 14 days, 2x daily limited sucrose
|
treatment protocol: 30% sucrose snack treatment
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Sucrose-BLA pooled from rats 4 and 10
|
| Sample_geo_accession | GSM509691
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509691/suppl/GSM509691.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509692 | GPL1355 |
|
BLA_sucrose_rep 5
|
BLA tissue after 14 days, 2x daily limited sucrose
|
treatment protocol: 30% sucrose snack treatment
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Sucrose-BLA pooled from rats 5 and 11
|
| Sample_geo_accession | GSM509692
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509692/suppl/GSM509692.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509693 | GPL1355 |
|
BLA_sucrose_rep 6
|
BLA tissue after 14 days, 2x daily limited sucrose
|
treatment protocol: 30% sucrose snack treatment
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Sucrose-BLA pooled from rats 6 and 12
|
| Sample_geo_accession | GSM509693
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509693/suppl/GSM509693.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509694 | GPL1355 |
|
BLA_Control_rep 1
|
BLA tissue after 14 days, 2x daily water control
|
treatment protocol: Control
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Control-BLA pooled from rats 13 and 19
|
| Sample_geo_accession | GSM509694
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509694/suppl/GSM509694.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509695 | GPL1355 |
|
BLA_Control_rep 2
|
BLA tissue after 14 days, 2x daily water control
|
treatment protocol: Control
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Control-BLA pooled from rats 14 and 20
|
| Sample_geo_accession | GSM509695
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509695/suppl/GSM509695.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509696 | GPL1355 |
|
BLA_Control_rep 3
|
BLA tissue after 14 days, 2x daily water control
|
treatment protocol: Control
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Control-BLA pooled from rats 15 and 21
|
| Sample_geo_accession | GSM509696
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509696/suppl/GSM509696.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509697 | GPL1355 |
|
BLA_Control_rep 4
|
BLA tissue after 14 days, 2x daily water control
|
treatment protocol: Control
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Control-BLA pooled from rats 16 and 22
|
| Sample_geo_accession | GSM509697
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509697/suppl/GSM509697.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509698 | GPL1355 |
|
BLA_Control_rep 5
|
BLA tissue after 14 days, 2x daily water control
|
treatment protocol: Control
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Control-BLA pooled from rats 17 and 23
|
| Sample_geo_accession | GSM509698
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509698/suppl/GSM509698.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
GSM509699 | GPL1355 |
|
BLA_Control_rep 6
|
BLA tissue after 14 days, 2x daily water control
|
treatment protocol: Control
tissue: basolateral amygdala
strain: Long-Evans
gender: male
age: 2-3 months
|
Control-BLA pooled from rats 18 and 24
|
| Sample_geo_accession | GSM509699
| | Sample_status | Public on Feb 17 2010
| | Sample_submission_date | Feb 16 2010
| | Sample_last_update_date | Feb 18 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Rats were given additional 2x daily access to 4mL of 30%sucrose for 14 days. The morning of day 15, rats were sacrificed by decapitation and the BLA was quickly dissected and placed in RNAlater (Ambion) and stored at -80°C until RNA extraction.
| | Sample_growth_protocol_ch1 | Housing protocol: Male, Long-Evans rats (225-250g) were single housed in shoebox cages and had free access to normal chow and water throughout the experiment
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen's mRNeasy extraction of total RNA was performed according to the manufacturer's instructions. Right and left BLA tissue was pooled from two animals of the same treatment group to make each sample.
| | Sample_extract_protocol_ch1 | Total RNA quality was verified using RNA 6000 Nano Assay, Agilent Bioanalyzer 2100 (Hewlett-Packard Company).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared using the TargetAmp 1-Round Aminoallyl-aRNA Amplification Kit (Epicentre Biotechnolgies) using TargetAmp t7-oligo(dT) primer A, Full Spectrum Multistart T7 IVT primers (SBI System Biosciences), and Biotin-X-X-NHS (Epicentre Biotechnologies).
| | Sample_hyb_protocol | cRNA was hybridized to Affymetrix microarray gene chips (Rat Genome 230 2.0 Array) according to the manufacturer's instructions.
| | Sample_scan_protocol | Genechips were visualized using R-phycoerythrin streptavidin (Invitrogen) and biotinylated anti-streptavidin antibody (Vector Laboratories) and scanned using Genechip operating software 1v4 on the Affymetrix GeneChip Scanner 3000.
| | Sample_data_processing | The data were analyzed by Cincinnati Children's Hospital Medical Center Biomedical Informatics Core using GeneSpring software (Agilent Technologies; Foster City, CA) version 7.3 using RMA normalization, then normalized to the mean of control samples. Hybridization controls included comparison of 3' and 5' probe sets for internal control genes and prokaryotic spike controls.
| | Sample_data_processing | Filters were applied to remove genes with little-to-no expression in the BLA (signal <100) and those that were not affected by treatment (fold change 0.8-1.2)
| | Sample_data_processing | Functional cluster analysis was performed on the list of 145 significantly upregulated genes using Ingenuity Pathway Analysis (Ingenuity Systems, Redwood City, CA). See supplementary file on Series GSE20344 record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Yvonne,,Ulrich-Lai
| | Sample_contact_email | ULRICHYM@UCMAIL.UC.EDU
| | Sample_contact_institute | University of Cincinnati
| | Sample_contact_address | 2170 E. Galbraith Rd. ML0506
| | Sample_contact_city | Cincinnati
| | Sample_contact_state | OH
| | Sample_contact_zip/postal_code | 45237
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM509nnn/GSM509699/suppl/GSM509699.CEL.gz
| | Sample_series_id | GSE20344
| | Sample_data_row_count | 31099
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
