Search results for the GEO ID: GSE34411  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM848732 | GPL1355 |
|
Neonatal aorta 1
|
proximal part neonatal rat aorta, collected within 24h after birth
|
tissue: neonatal aorta
strain: Wistar
|
Gene expression from neonatal aortas, early neonatal development (<24h after birth)
|
| Sample_geo_accession | GSM848732
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848732/suppl/GSM848732.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848732/suppl/GSM848732.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848733 | GPL1355 |
|
Neonatal aorta 2
|
proximal part neonatal rat aorta, collected within 24h after birth
|
tissue: neonatal aorta
strain: Wistar
|
Gene expression from neonatal aortas, early neonatal development (<24h after birth)
|
| Sample_geo_accession | GSM848733
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848733/suppl/GSM848733.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848733/suppl/GSM848733.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848734 | GPL1355 |
|
Neonatal aorta 3
|
proximal part neonatal rat aorta, collected within 24h after birth
|
tissue: neonatal aorta
strain: Wistar
|
Gene expression from neonatal aortas, early neonatal development (<24h after birth)
|
| Sample_geo_accession | GSM848734
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848734/suppl/GSM848734.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848734/suppl/GSM848734.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848735 | GPL1355 |
|
Adult aorta1
|
proximal part adult rat aorta, male
|
tissue: neonatal semilunar valve
strain: Wistar
|
Gene expression from neonatal semilunar valves, early neonatal development (<24h after birth)
|
| Sample_geo_accession | GSM848735
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848735/suppl/GSM848735.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848735/suppl/GSM848735.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848736 | GPL1355 |
|
Adult aorta2
|
proximal part adult rat aorta, male
|
tissue: neonatal semilunar valve
strain: Wistar
|
Gene expression from neonatal semilunar valves, early neonatal development (<24h after birth)
|
| Sample_geo_accession | GSM848736
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848736/suppl/GSM848736.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848736/suppl/GSM848736.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848737 | GPL1355 |
|
Adult aorta3
|
proximal part adult rat aorta, male
|
tissue: neonatal semilunar valve
strain: Wistar
|
Gene expression from neonatal semilunar valves, early neonatal development (<24h after birth)
|
| Sample_geo_accession | GSM848737
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848737/suppl/GSM848737.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848737/suppl/GSM848737.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848738 | GPL1355 |
|
Neonatal valve 1
|
neonatal rat semilunar valves (aortic and pulmonary), collected within 24h after birth
|
tissue: adult aorta
strain: Wistar
|
Gene expression from adult aortas, steady-state tissue
|
| Sample_geo_accession | GSM848738
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848738/suppl/GSM848738.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848738/suppl/GSM848738.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848739 | GPL1355 |
|
Neonatal valve 2
|
neonatal rat semilunar valves (aortic and pulmonary), collected within 24h after birth
|
tissue: adult aorta
strain: Wistar
|
Gene expression from adult aortas, steady-state tissue
|
| Sample_geo_accession | GSM848739
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848739/suppl/GSM848739.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848739/suppl/GSM848739.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848740 | GPL1355 |
|
Neonatal valve 3
|
neonatal rat semilunar valves (aortic and pulmonary), collected within 24h after birth
|
tissue: adult aorta
strain: Wistar
|
Gene expression from adult aortas, steady-state tissue
|
| Sample_geo_accession | GSM848740
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848740/suppl/GSM848740.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848740/suppl/GSM848740.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848741 | GPL1355 |
|
Adult valve 1
|
adult rat semilunar valves (aortic and pulmonary), male
|
tissue: adult semilunar valve
strain: Wistar
|
Gene expression from adult semilunar valves, steady-state tissue
|
| Sample_geo_accession | GSM848741
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848741/suppl/GSM848741.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848741/suppl/GSM848741.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848742 | GPL1355 |
|
Adult valve 2
|
adult rat semilunar valves (aortic and pulmonary), male
|
tissue: adult semilunar valve
strain: Wistar
|
Gene expression from adult semilunar valves, steady-state tissue
|
| Sample_geo_accession | GSM848742
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848742/suppl/GSM848742.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848742/suppl/GSM848742.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
GSM848743 | GPL1355 |
|
Adult valve 3
|
adult rat semilunar valves (aortic and pulmonary), male
|
tissue: adult semilunar valve
strain: Wistar
|
Gene expression from adult semilunar valves, steady-state tissue
|
| Sample_geo_accession | GSM848743
| | Sample_status | Public on Dec 14 2011
| | Sample_submission_date | Dec 13 2011
| | Sample_last_update_date | Dec 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from both neonatal and adult rat aortae (proximal part) and semilunar valves (aortic and pulmonary) using Trizol (Invitrogen, CA, USA) and RNeasy Mini RNA isolation columns (Qiagen, Hilden, Germany) following the protocol of the University of Nebraska Medical Center Microarray Core Facility (http://www.unmc.edu/microarray).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The poly-A RNA was labeled during a T7 in vitro transcription reaction using the Affymetrix IVT Labeling Kit
| | Sample_hyb_protocol | The fragmented amplified RNA (aRNA) was resuspended with control spikes in 300 µl hybridization buffer using the Eukaryotic Hybridization Control Kit (Affymetrix, UK) and 200 µl probe was hybridized in a rotisserie oven at 45°C.
| | Sample_scan_protocol | scanned with the GeneChip Scanner 3000
| | Sample_data_processing | The acquired raw data (.CEL files) were uploaded onto the Affymetrix Expression Console Software (ECS). The Microarray Suite Statistical Algorithm (MAS5.0) was applied for single array or absolute analysis. This algorithm uses the Tukey’s biweight estimator to provide a robust mean signal value and the Wilcoxon’s rank test combined with a Spearman Rank Correlation (which was preferred over Pearson’s Correlation, because of the limited sample number) to calculate a detection significance or p-value and detection call for each probe set. Mismatch probes were utilized to adjust the perfect match intensity. Arrays were analyzed independently of each other using MAS5.0. The detection p-value was used to determine the absolute detection call for probe sets: a call “Present” (P) was assigned to transcripts with a p-value smaller than 0.04 and a call “Absent” (A) was assigned to transcripts with a p-value between 0.04 and 1. In each individual array, probe sets with A calls were excluded from further comparison data analysis.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Geofrey,,De Visscher
| | Sample_contact_institute | KULeuven
| | Sample_contact_address | Minderbroedersstraat 12 Building P
| | Sample_contact_city | Leuven
| | Sample_contact_zip/postal_code | 3000
| | Sample_contact_country | Belgium
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848743/suppl/GSM848743.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM848nnn/GSM848743/suppl/GSM848743.CHP.gz
| | Sample_series_id | GSE34411
| | Sample_data_row_count | 31099
| | |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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