Search results for the GEO ID: GSE42930  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1053519 | GPL1261 |
|
APOE3, replicate 1
|
liver, APOE3
|
strain/background: C57BL/6
genotype/variation: APOE3 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E3 12
|
| Sample_geo_accession | GSM1053519
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053519/suppl/GSM1053519_2008-11-28_12.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053520 | GPL1261 |
|
APOE3, replicate 2
|
liver, APOE3
|
strain/background: C57BL/6
genotype/variation: APOE3 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E3 39
|
| Sample_geo_accession | GSM1053520
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053520/suppl/GSM1053520_2008-11-28_39.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053521 | GPL1261 |
|
APOE3, replicate 3
|
liver, APOE3
|
strain/background: C57BL/6
genotype/variation: APOE3 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E3 48
|
| Sample_geo_accession | GSM1053521
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053521/suppl/GSM1053521_2008-11-28_48.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053522 | GPL1261 |
|
APOE3, replicate 4
|
liver, APOE3
|
strain/background: C57BL/6
genotype/variation: APOE3 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E3 66
|
| Sample_geo_accession | GSM1053522
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053522/suppl/GSM1053522_2008-11-28_66.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053523 | GPL1261 |
|
APOE3, replicate 5
|
liver, APOE3
|
strain/background: C57BL/6
genotype/variation: APOE3 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E3 75
|
| Sample_geo_accession | GSM1053523
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053523/suppl/GSM1053523_2008-11-28_75.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053524 | GPL1261 |
|
APOE4, replicate 1
|
liver, APOE4
|
strain/background: C57BL/6
genotype/variation: APOE4 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E4 2
|
| Sample_geo_accession | GSM1053524
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053524/suppl/GSM1053524_2008-11-28_2.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053525 | GPL1261 |
|
APOE4, replicate 2
|
liver, APOE4
|
strain/background: C57BL/6
genotype/variation: APOE4 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E4 27
|
| Sample_geo_accession | GSM1053525
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053525/suppl/GSM1053525_2008-11-28_27.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053526 | GPL1261 |
|
APOE4, replicate 3
|
liver, APOE4
|
strain/background: C57BL/6
genotype/variation: APOE4 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E4 47
|
| Sample_geo_accession | GSM1053526
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053526/suppl/GSM1053526_2008-11-28_47.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053527 | GPL1261 |
|
APOE4, replicate 4
|
liver, APOE4
|
strain/background: C57BL/6
genotype/variation: APOE4 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E4 56
|
| Sample_geo_accession | GSM1053527
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053527/suppl/GSM1053527_2008-11-28_56.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
|
GSM1053528 | GPL1261 |
|
APOE4, replicate 5
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liver, APOE4
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strain/background: C57BL/6
genotype/variation: APOE4 targeted gene replacement
gender: female
age: 3 months
tissue: liver
|
E4 65
|
| Sample_geo_accession | GSM1053528
| | Sample_status | Public on Dec 15 2012
| | Sample_submission_date | Dec 14 2012
| | Sample_last_update_date | Dec 15 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_growth_protocol_ch1 | Female targeted gene replacement (TR) mice expressing the human APOE isoforms under the regulatory control of the murine Apoe promoter on a C57BL/6 background were purchased from Taconic Europe (Ry, Denmark). The mice were fed a semi-synthetic diet based on corn starch (14.5%), casein (17.1%), sucrose (32.8%) and butter fat (21.2%), containing 0.2% cholesterol for 2 months.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total liver RNA was isolated with TRIsure (Bioline, Luckenwalde, Germany) using chloroform/water separation and isopropyl alcohol precipitation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotin-labeled cRNA was synthesized from 2 µg RNA using the MessageAmp II-Biotin Enhanced Kit (Ambion/Applied Biosystems, Darmstadt, Germany) including poly-A RNA controls (GeneChipw Eukaryotic Poly-A RNA Control Kit) according to the manufacturer's instructions.
| | Sample_hyb_protocol | 10 Mouse Genome 430 2.0 GeneChip® microarrays were hybridised for 16 h at 45C with 15 ug fragmented, biotin-labelled cRNA each, including hybridisation controls (GeneChip® Eukaryotic Hybridization Control Kit), using a Hybridization Oven 640 and following the manufacturer's instructions (GeneChip® Expression Analysis Technical Manual, P/N 702232 Rev. 2). Microarrays were subsequently washed and stained using a Fluidics Station 450 and the FS450_0004 script.
| | Sample_scan_protocol | GeneChip® Scanner 3000 using the GCOS software.
| | Sample_data_processing | Quality control and normalisation of CEL data based on the Affymetrix chip definition file were performed with R software (version 2.7.1) and BioConductor (version 2.0.1) with the package ‘simpleaffy’ (version 2.16.0-1) as provided by the MADMAX database (https://madmax.bioinformatics.nl/pls/apex/wwv_flow_file_mgr.get_file?p_security_group_id=723402266026950&p_fname=About_MADMAX.pdf). Data were normalised with the GC-RMA algorithm and background correction based on empirical Bayes estimate (GC-RMA slow, 'gcrma' package version 2.12.1).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Gregor,,Warsow
| | Sample_contact_laboratory | IBIMA
| | Sample_contact_department | Medical Department
| | Sample_contact_institute | University of Rostock
| | Sample_contact_address | Ernst-Heydemann-Str. 8
| | Sample_contact_city | Rostock
| | Sample_contact_zip/postal_code | 18057
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1053nnn/GSM1053528/suppl/GSM1053528_2008-11-28_65.CEL.gz
| | Sample_series_id | GSE42930
| | Sample_data_row_count | 45101
| | |
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