Search results for the GEO ID: GSE11476  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM289058 | GPL341 |
|
Control CA3, biological rep1
|
RNA from CA3 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289058
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289058/suppl/GSM289058.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289059 | GPL341 |
|
Control CA3, biological rep2
|
RNA from CA3 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289059
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289059/suppl/GSM289059.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289060 | GPL341 |
|
Control CA3, biological rep3
|
RNA from CA3 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289060
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289060/suppl/GSM289060.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289061 | GPL341 |
|
Control CA3, biological rep4
|
RNA from CA3 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289061
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289061/suppl/GSM289061.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289062 | GPL341 |
|
Control CA3, biological rep5
|
RNA from CA3 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289062
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289062/suppl/GSM289062.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289063 | GPL341 |
|
Control CA3, biological rep6
|
RNA from CA3 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289063
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289063/suppl/GSM289063.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289064 | GPL341 |
|
Control CA3, biological rep7
|
RNA from CA3 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289064
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289064/suppl/GSM289064.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289065 | GPL341 |
|
Learning Activated CA3, biological rep1
|
RNA from CA3 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289065
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289065/suppl/GSM289065.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289066 | GPL341 |
|
Learning Activated CA3, biological rep2
|
RNA from CA3 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289066
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289066/suppl/GSM289066.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289067 | GPL341 |
|
Learning Activated CA3, biological rep3
|
RNA from CA3 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289067
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289067/suppl/GSM289067.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289068 | GPL341 |
|
Learning Activated CA3, biological rep4
|
RNA from CA3 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289068
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289068/suppl/GSM289068.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289069 | GPL341 |
|
Learning Activated CA3, biological rep5
|
RNA from CA3 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289069
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289069/suppl/GSM289069.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289070 | GPL341 |
|
Learning Activated CA3, biological rep6
|
RNA from CA3 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289070
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289070/suppl/GSM289070.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289071 | GPL341 |
|
Learning Activated CA3, biological rep7
|
RNA from CA3 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289071
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289071/suppl/GSM289071.CEL.gz
| | Sample_series_id | GSE11473
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289072 | GPL341 |
|
Control CA1, biological rep1
|
RNA from CA1 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289072
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289072/suppl/GSM289072.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289073 | GPL341 |
|
Control CA1, biological rep2
|
RNA from CA1 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289073
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289073/suppl/GSM289073.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289074 | GPL341 |
|
Control CA1, biological rep3
|
RNA from CA1 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289074
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289074/suppl/GSM289074.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289075 | GPL341 |
|
Control CA1, biological rep4
|
RNA from CA1 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289075
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289075/suppl/GSM289075.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289076 | GPL341 |
|
Control CA1, biological rep5
|
RNA from CA1 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289076
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289076/suppl/GSM289076.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289077 | GPL341 |
|
Control CA1, biological rep6
|
RNA from CA1 region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289077
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289077/suppl/GSM289077.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289078 | GPL341 |
|
Learning Activated CA1, biological rep1
|
RNA from CA1 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289078
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289078/suppl/GSM289078.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289079 | GPL341 |
|
Learning Activated CA1, biological rep2
|
RNA from CA1 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289079
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289079/suppl/GSM289079.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289080 | GPL341 |
|
Learning Activated CA1, biological rep3
|
RNA from CA1 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289080
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289080/suppl/GSM289080.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289081 | GPL341 |
|
Learning Activated CA1, biological rep4
|
RNA from CA1 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289081
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289081/suppl/GSM289081.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289082 | GPL341 |
|
Learning Activated CA1, biological rep5
|
RNA from CA1 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289082
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289082/suppl/GSM289082.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289083 | GPL341 |
|
Learning Activated CA1, biological rep6
|
RNA from CA1 region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289083
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289083/suppl/GSM289083.CEL.gz
| | Sample_series_id | GSE11474
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289084 | GPL341 |
|
Control DG, biological rep1
|
RNA from DG region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289084
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289084/suppl/GSM289084.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289085 | GPL341 |
|
Control DG, biological rep2
|
RNA from DG region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289085
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289085/suppl/GSM289085.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289086 | GPL341 |
|
Control DG, biological rep3
|
RNA from DG region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289086
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289086/suppl/GSM289086.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289087 | GPL341 |
|
Control DG, biological rep4
|
RNA from DG region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289087
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289087/suppl/GSM289087.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289088 | GPL341 |
|
Control DG, biological rep5
|
RNA from DG region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289088
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289088/suppl/GSM289088.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289089 | GPL341 |
|
Control DG, biological rep6
|
RNA from DG region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289089
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289089/suppl/GSM289089.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289090 | GPL341 |
|
Control DG, biological rep7
|
RNA from DG region of the hippocampus following control task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289090
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289090/suppl/GSM289090.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289091 | GPL341 |
|
Learning Activated DG, biological rep1
|
RNA from DG region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289091
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289091/suppl/GSM289091.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289092 | GPL341 |
|
Learning Activated DG, biological rep2
|
RNA from DG region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289092
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289092/suppl/GSM289092.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289093 | GPL341 |
|
Learning Activated DG, biological rep3
|
RNA from DG region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289093
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289093/suppl/GSM289093.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289094 | GPL341 |
|
Learning Activated DG, biological rep4
|
RNA from DG region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289094
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289094/suppl/GSM289094.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289095 | GPL341 |
|
Learning Activated DG, biological rep5
|
RNA from DG region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289095
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289095/suppl/GSM289095.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289096 | GPL341 |
|
Learning Activated DG, biological rep6
|
RNA from DG region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289096
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289096/suppl/GSM289096.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
GSM289097 | GPL341 |
|
Learning Activated DG, biological rep7
|
RNA from DG region of the hippocampus following spatial learning task
|
Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM289097
| | Sample_status | Public on Jun 01 2008
| | Sample_submission_date | May 16 2008
| | Sample_last_update_date | May 19 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | All rats received the same standard water maze spatial training as detailed in Gallagher et al (Gallagher, M., Burwell, R. & Burchinal, M. 1993. Severity of spatial learning impairment in aging: development of a learning index for performance in the Morris water maze. Behav Neurosci 107, 618-26.). After 2-3 weeks, the rats were given a single training session (8 trials with 8-min ITI) in a new water maze environment located at a different site. The LA group received training in the presence of orienting spatial cues and in which a visible escape platform remained at the same location. The CTL group received training in which the location of the visible platform varied across the trials and the environment lacked any informative orienting cues. One hour after the last training trial, all rats were given 90-sec probe trial without the escape platform. Data were analyzed with a video tracking system (HVS Image Analyzing VP-116) and an IBM PC computer with software developed by HVS Imaging (Hampton, UK).
| | Sample_growth_protocol_ch1 | Young (3-4 months old) male Long-Evans rats (Charles River Laboratories, Raleigh, NC) were individually housed on a 12:12-hr light/dark cycle with ad libitum access to food and water. Animals were then exposed to a behavioral paradigm.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Rats were sacrificed immediately after the probe trial. The CA1, CA3 and DG regions of the hippocampus were microdissected from the hippocampus and total RNA was extracted by homogenization in Trizol reagent (Invitrogen) followed by application to Qiagen RNeasy columns.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA samples were sent to the Johns Hopkins Microarray core facility for cRNA labeling, and hybridization to Affymetrix RAE230A microarrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on RAE230a GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
| | Sample_data_processing | All quality control, normalization, differential expression, and exploratory analysis of microarray data were performed using the R statistical language (http://www.r-project.org/). The gcrma package in Bioconductor (http://www.bioconductor.org/) was used to normalize microarray data and mild biases in mean ratios across intensity were balanced using a loess function in R.
| | Sample_platform_id | GPL341
| | Sample_contact_name | Carlo,,Colantuoni
| | Sample_contact_email | carlo.colantuoni@libd.org
| | Sample_contact_laboratory | Genome Informatics
| | Sample_contact_department | Developmental Neurobiology and Functional Genomics
| | Sample_contact_institute | Lieber Institute for Brain Development
| | Sample_contact_address | 855 N. Wolfe St., Room 327
| | Sample_contact_city | Baltimore
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 21205
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM289nnn/GSM289097/suppl/GSM289097.CEL.gz
| | Sample_series_id | GSE11475
| | Sample_series_id | GSE11476
| | Sample_data_row_count | 15923
| | |
|
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