Search results for the GEO ID: GSE27888  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM688773 | GPL1261 |
|
APLP2_cortex_rep1
|
Prefrontal cortex from adult APLP2 knock-out mouse
|
tissue: prefrontal cortex
background strain: C57BL/6
gender: female
genotype/variation: APLP2-KO (APLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688773
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688773/suppl/GSM688773.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688774 | GPL1261 |
|
APLP2_hippocampus_rep1
|
Hippocampus from adult APLP2 knock-out mouse
|
tissue: hippocampus
background strain: C57BL/6
gender: female
genotype/variation: APLP2-KO (APLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688774
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688774/suppl/GSM688774.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688775 | GPL1261 |
|
APLP2_cortex_rep2
|
Prefrontal cortex from adult APLP2 knock-out mouse
|
tissue: prefrontal cortex
background strain: C57BL/6
gender: female
genotype/variation: APLP2-KO (APLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688775
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688775/suppl/GSM688775.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688776 | GPL1261 |
|
APLP2_hippocampus_rep2
|
Hippocampus from adult APLP2 knock-out mouse
|
tissue: hippocampus
background strain: C57BL/6
gender: female
genotype/variation: APLP2-KO (APLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688776
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688776/suppl/GSM688776.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688777 | GPL1261 |
|
APLP2_cortex_rep3
|
Prefrontal cortex from adult APLP2 knock-out mouse
|
tissue: prefrontal cortex
background strain: C57BL/6
gender: female
genotype/variation: APLP2-KO (APLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688777
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688777/suppl/GSM688777.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688778 | GPL1261 |
|
APLP2_hippocampus_rep3
|
Hippocampus from adult APLP2 knock-out mouse
|
tissue: hippocampus
background strain: C57BL/6
gender: female
genotype/variation: APLP2-KO (APLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688778
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688778/suppl/GSM688778.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688779 | GPL1261 |
|
APPsa-DM_cortex_rep1
|
Prefrontal cortex from adult APPsα-DM mouse
|
tissue: prefrontal cortex
background strain: C57BL/6
gender: female
genotype/variation: APPsα-DM (APPα/αAPLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688779
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688779/suppl/GSM688779.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688780 | GPL1261 |
|
APPsa-DM_hippocampus_rep1
|
Hippocampus from adult APPsα-DM knock-out mouse
|
tissue: hippocampus
background strain: C57BL/6
gender: female
genotype/variation: APPsα-DM (APPα/αAPLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688780
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688780/suppl/GSM688780.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688781 | GPL1261 |
|
APPsa-DM_cortex_rep2
|
Prefrontal cortex from adult APPsα-DM mouse
|
tissue: prefrontal cortex
background strain: C57BL/6
gender: female
genotype/variation: APPsα-DM (APPα/αAPLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688781
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688781/suppl/GSM688781.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688782 | GPL1261 |
|
APPsa-DM_hippocampus_rep2
|
Hippocampus from adult APPsα-DM knock-out mouse
|
tissue: hippocampus
background strain: C57BL/6
gender: female
genotype/variation: APPsα-DM (APPα/αAPLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688782
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688782/suppl/GSM688782.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
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GSM688783 | GPL1261 |
|
APPsa-DM_cortex_rep3
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Prefrontal cortex from adult APPsα-DM mouse
|
tissue: prefrontal cortex
background strain: C57BL/6
gender: female
genotype/variation: APPsα-DM (APPα/αAPLP2-/-)
age: adult (38 - 40 weeks)
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back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688783
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688783/suppl/GSM688783.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
|
GSM688784 | GPL1261 |
|
APPsa-DM_hippocampus_rep3
|
Hippocampus from adult APPsα-DM knock-out mouse
|
tissue: hippocampus
background strain: C57BL/6
gender: female
genotype/variation: APPsα-DM (APPα/αAPLP2-/-)
age: adult (38 - 40 weeks)
|
back-crossed to C57BL/6 for 6 generations
|
| Sample_geo_accession | GSM688784
| | Sample_status | Public on May 10 2011
| | Sample_submission_date | Mar 10 2011
| | Sample_last_update_date | May 10 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Animals were sacrificed by cervical dislocation. Dissected brains were stored at -20°C in RNAlater (Qiagen). Subsequently, prefrontal cortices and hippocampi were dissected.
| | Sample_growth_protocol_ch1 | Animals were kept under specific pathogen free housing conditions (SPF unit) and in compliance with the regulations of the German animal protection law.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using the RNAeasy kit from Qiagen and following the manufacturer's recommendations. RNA quality was assessed with the Bioanalyzer 2100 (Agilent) to ensure high sample quality across all samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1µg total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15µg cRNA were hybridized for 16 hr at 45°C on Affymetrix Mouse Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data was processed in R using the RMA algorithm including RMA background correction, quantile normalization, and median polish as summarization method implemented in the affy package and provided by Bioconductor.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Ulrike,,Müller
| | Sample_contact_email | u.mueller@urz.uni-hd.de
| | Sample_contact_department | Bioinformatics and Functional Genomics
| | Sample_contact_institute | Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg
| | Sample_contact_address | Im Neuenheimer Feld 364
| | Sample_contact_city | Heidelberg
| | Sample_contact_zip/postal_code | 69120
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM688nnn/GSM688784/suppl/GSM688784.CEL.gz
| | Sample_series_id | GSE27888
| | Sample_data_row_count | 45101
| | |
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