Search results for the GEO ID: GSE14723  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM367827 | GPL1355 |
|
Aged Impaired CA1, biological rep1
|
RNA from CA1 region of the hippocampus: Aged Impaired
|
aged (24-26 months old) cognitively impaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367827
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367827/suppl/GSM367827.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367828 | GPL1355 |
|
Aged Impaired CA1, biological rep2
|
RNA from CA1 region of the hippocampus: Aged Impaired
|
aged (24-26 months old) cognitively impaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367828
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367828/suppl/GSM367828.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367829 | GPL1355 |
|
Aged Impaired CA1, biological rep3
|
RNA from CA1 region of the hippocampus: Aged Impaired
|
aged (24-26 months old) cognitively impaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367829
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367829/suppl/GSM367829.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367830 | GPL1355 |
|
Aged Impaired CA1, biological rep4
|
RNA from CA1 region of the hippocampus: Aged Impaired
|
aged (24-26 months old) cognitively impaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367830
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367830/suppl/GSM367830.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367831 | GPL1355 |
|
Aged Impaired CA1, biological rep5
|
RNA from CA1 region of the hippocampus: Aged Impaired
|
aged (24-26 months old) cognitively impaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367831
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367831/suppl/GSM367831.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367832 | GPL1355 |
|
Aged Impaired CA1, biological rep6
|
RNA from CA1 region of the hippocampus: Aged Impaired
|
aged (24-26 months old) cognitively impaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367832
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367832/suppl/GSM367832.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367833 | GPL1355 |
|
Aged Impaired CA1, biological rep7
|
RNA from CA1 region of the hippocampus: Aged Impaired
|
aged (24-26 months old) cognitively impaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367833
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367833/suppl/GSM367833.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367834 | GPL1355 |
|
Aged Impaired CA1, biological rep8
|
RNA from CA1 region of the hippocampus: Aged Impaired
|
aged (24-26 months old) cognitively impaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367834
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367834/suppl/GSM367834.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367835 | GPL1355 |
|
Aged Unimpaired CA1, biological rep1
|
RNA from CA1 region of the hippocampus: Aged Unimpaired
|
aged (24-26 months old) cognitively unimpaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367835
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367835/suppl/GSM367835.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367836 | GPL1355 |
|
Aged Unimpaired CA1, biological rep2
|
RNA from CA1 region of the hippocampus: Aged Unimpaired
|
aged (24-26 months old) cognitively unimpaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367836
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367836/suppl/GSM367836.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367837 | GPL1355 |
|
Aged Unimpaired CA1, biological rep3
|
RNA from CA1 region of the hippocampus: Aged Unimpaired
|
aged (24-26 months old) cognitively unimpaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367837
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367837/suppl/GSM367837.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367838 | GPL1355 |
|
Aged Unimpaired CA1, biological rep4
|
RNA from CA1 region of the hippocampus: Aged Unimpaired
|
aged (24-26 months old) cognitively unimpaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367838
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367838/suppl/GSM367838.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367839 | GPL1355 |
|
Aged Unimpaired CA1, biological rep5
|
RNA from CA1 region of the hippocampus: Aged Unimpaired
|
aged (24-26 months old) cognitively unimpaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367839
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367839/suppl/GSM367839.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367840 | GPL1355 |
|
Young CA1, biological rep9
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367840
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367840/suppl/GSM367840.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367841 | GPL1355 |
|
Aged Unimpaired CA1, biological rep7
|
RNA from CA1 region of the hippocampus: Aged Unimpaired
|
aged (24-26 months old) cognitively unimpaired 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367841
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367841/suppl/GSM367841.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367842 | GPL1355 |
|
Aged Unimpaired CA1, biological rep8
|
RNA from CA1 region of the hippocampus: Aged Unimpaired
|
aged (24-26 months old) cognitively unimpaired 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.
|
this array/sample was omitted from the study as a result of quality control procedures
|
| Sample_geo_accession | GSM367842
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367842/suppl/GSM367842.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 0
| | |
|
GSM367843 | GPL1355 |
|
Young CA1, biological rep1
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367843
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367843/suppl/GSM367843.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367844 | GPL1355 |
|
Young CA1, biological rep2
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367844
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367844/suppl/GSM367844.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367845 | GPL1355 |
|
Young CA1, biological rep3
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367845
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367845/suppl/GSM367845.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367846 | GPL1355 |
|
Young CA1, biological rep4
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367846
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367846/suppl/GSM367846.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367847 | GPL1355 |
|
Young CA1, biological rep5
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367847
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367847/suppl/GSM367847.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367848 | GPL1355 |
|
Young CA1, biological rep6
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367848
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367848/suppl/GSM367848.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367849 | GPL1355 |
|
Young CA1, biological rep7
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367849
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367849/suppl/GSM367849.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
| | |
|
GSM367850 | GPL1355 |
|
Young CA1, biological rep8
|
RNA from CA1 region of the hippocampus: Young
|
young (6 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.
|
Hippocampal RNA
|
| Sample_geo_accession | GSM367850
| | Sample_status | Public on Nov 01 2009
| | Sample_submission_date | Feb 05 2009
| | Sample_last_update_date | Oct 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There was no treatment. Three groups of rats were defined by age and cognitive staus: Young, Aged Unimpaired, and Aged Impaired. Behavioral assessment of memory function in a Morris water maze task was conducted as previously described (Gallagher et al., 1993). A learning index was generated from the proximity of the rat to the escape platform during probe trials interpolated throughout training and was used to define impairment in the rats. Low scores reflect good performance and aged rats performing within the range of young are designated aged unimpaired (AU) whereas those performing worse than young are considered aged impaired (AI).
| | Sample_growth_protocol_ch1 | Aged, male Long-Evans rats were obtained at 8-9 mo of age from Charles River Laboratories (Raleigh, NC) and housed in a vivarium at The Johns Hopkins University until 24-26 mo of age for the present experiments. Young rats at 6 months of age were tested alongside the aged rats. All rats were individually housed at 25°C and maintained on a 12 hr light/dark cycle. Food and water were provided ad libitum. The rats were examined for health and pathogen-free status throughout the experiments, as well as by necropsies at the time of sacrifice. All procedures were approved by the institutional animal care and use committee in accordance with the National Institutes of Health directive.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | All rats were sacrificed two weeks after completion of behavioral testing by rapid decapitation, and brains removed from the skull. 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 GeneChip Rat Genome 230 2.0 arrays using standard Affymetrix recommended procedures.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip Rat Genome 230 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 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 a batch effect resulting from microarray processing procedures was removed individually from each probe set signal by simple subtraction of the mean difference of each batch to the grand mean (Batch#1 samples: RHab-HCA-AICA1_21-1a-RAE230_2, RHab-HCA-AICA1_22-1a-RAE230_2, RHab-HCA-AICA1_23-1a-RAE230_2,RHab-HCA-AICA1_24-1a_2-RAE230_2, RHab-HCA-AUCA1_13-1a-RAE230_2, RHab-HCA-AUCA1_14-1a-RAE230_2, RHab-HCA-AUCA1_15-1a-RAE230_2, RHab-HCA-YCA1_5-1a_2-RAE230_2, RHab-HCA-YCA1_6-1a_2-RAE230_2,RHab-HCA-YCA1_7-1a-RAE230_2, RHab-HCA-YCA1_8-1a-RAE230_2. Batch#2 samples: RHab-HCA-AICA1_17-1a-RAE230_2, RHab-HCA-AICA1_18-1a-RAE230_2, RHab-HCA-AICA1_19-1a_2-RAE230_2, RHab-HCA-AICA1_20-1a_2-RAE230_2, RHab-HCA-AUCA1_10-1a_2-RAE230_2, RHab-HCA-AUCA1_11-1a-RAE230_2, RHab-HCA-AUCA1_12-1a-RAE230_2, RHab-HCA-AUCA1_9-1a-RAE230_2, RHab-HCA-YCA1_1-1a-RAE230_2,RHab-HCA-YCA1_2-1a-RAE230_2, RHab-HCA-YCA1_3-1a-RAE230_2, RHab-HCA-YCA1_4-1a_2-RAE230_2). Sample RHab-HCA-AUCA1_16-1a-RAE230_2 was omitted from the study as a result of quality control procedures.
| | Sample_platform_id | GPL1355
| | 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/GSM367nnn/GSM367850/suppl/GSM367850.CEL.gz
| | Sample_series_id | GSE14723
| | Sample_series_id | GSE14726
| | Sample_data_row_count | 31099
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