Search results for the GEO ID: GSE5606  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM130860 | GPL1355 |
|
LVHeart_Normal195_16wks, biological rep1
|
control (no diabetes), left ventricle (LV) heart tissue, 16wks
|
Wistar, control animal, saline injection, left ventricle heart tissue
|
Gene expression data from LV heart tissue of normal animal 16wks after saline injection
|
| Sample_geo_accession | GSM130860
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Controls (normal) were anaesthetised (Halothane 2-5%) and received a tail vein injection of saline (0.3-0.5 mL final volume). Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130860/suppl/GSM130860.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130861 | GPL1355 |
|
LVHeart_Normal030_16wks, biological rep2
|
control (no diabetes), left ventricle (LV) heart tissue, 16wks
|
Wistar, control animal, saline injection, left ventricle heart tissue
|
Gene expression data from LV heart tissue of normal animal 16wks after saline injection
|
| Sample_geo_accession | GSM130861
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Controls (normal) were anaesthetised (Halothane 2-5%) and received a tail vein injection of saline (0.3-0.5 mL final volume). Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130861/suppl/GSM130861.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130862 | GPL1355 |
|
LVHeart_Normal060_16wks, biological rep3
|
control (no diabetes), left ventricle (LV) heart tissue, 16wks
|
Wistar, control animal, saline injection, left ventricle heart tissue
|
Gene expression data from LV heart tissue of normal animal 16wks after saline injection
|
| Sample_geo_accession | GSM130862
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Controls (normal) were anaesthetised (Halothane 2-5%) and received a tail vein injection of saline (0.3-0.5 mL final volume). Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130862/suppl/GSM130862.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130863 | GPL1355 |
|
LVHeart_Normal153_16wks, biological rep4
|
control (no diabetes), left ventricle (LV) heart tissue, 16wks
|
Wistar, control animal, saline injection, left ventricle heart tissue
|
Gene expression data from LV heart tissue of normal animal 16wks after saline injection
|
| Sample_geo_accession | GSM130863
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Controls (normal) were anaesthetised (Halothane 2-5%) and received a tail vein injection of saline (0.3-0.5 mL final volume). Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130863/suppl/GSM130863.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130864 | GPL1355 |
|
LVHeart_Normal260_16wks, biological rep5
|
control (no diabetes), left ventricle (LV) heart tissue, 16wks
|
Wistar, control animal, saline injection, left ventricle heart tissue
|
Gene expression data from LV heart tissue of normal animal 16wks after saline injection
|
| Sample_geo_accession | GSM130864
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Controls (normal) were anaesthetised (Halothane 2-5%) and received a tail vein injection of saline (0.3-0.5 mL final volume). Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130864/suppl/GSM130864.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130865 | GPL1355 |
|
LVHeart_Normal791_16wks, biological rep6
|
control (no diabetes), left ventricle (LV) heart tissue, 16wks
|
Wistar, control animal, saline injection, left ventricle heart tissue
|
Gene expression data from LV heart tissue of normal animal 16wks after saline injection
|
| Sample_geo_accession | GSM130865
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Controls (normal) were anaesthetised (Halothane 2-5%) and received a tail vein injection of saline (0.3-0.5 mL final volume). Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130865/suppl/GSM130865.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130866 | GPL1355 |
|
LVHeart_Normal796_16wks, biological rep7
|
control (no diabetes), left ventricle (LV) heart tissue, 16wks
|
Wistar, control animal, saline injection, left ventricle heart tissue
|
Gene expression data from LV heart tissue of normal animal 16wks after saline injection
|
| Sample_geo_accession | GSM130866
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Controls (normal) were anaesthetised (Halothane 2-5%) and received a tail vein injection of saline (0.3-0.5 mL final volume). Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130866/suppl/GSM130866.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130867 | GPL1355 |
|
LVHeart_Diabetic035_16wks, biological rep1
|
Diabetic, left ventricle (LV) heart tissue, 16wks
|
Wistar, diabetic animal, STZ injection, left ventricle heart tissue, blood glucose level >15mM for the duration of the study
|
Gene expression data from LV heart tissue of diabetic animal 16wks after saline injection
|
| Sample_geo_accession | GSM130867
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Male wistars were anaesthetised (Halothane 2-5%) and received a tail vein injection of STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130867/suppl/GSM130867.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130868 | GPL1355 |
|
LVHeart_Diabetic370_16wks, biological rep2
|
Diabetic, left ventricle (LV) heart tissue, 16wks
|
Wistar, diabetic animal, STZ injection, left ventricle heart tissue, blood glucose level >15mM for the duration of the study
|
Gene expression data from LV heart tissue of diabetic animal 16wks after saline injection
|
| Sample_geo_accession | GSM130868
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Male wistars were anaesthetised (Halothane 2-5%) and received a tail vein injection of STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130868/suppl/GSM130868.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130869 | GPL1355 |
|
LVHeart_Diabetic481_16wks, biological rep3
|
Diabetic, left ventricle (LV) heart tissue, 16wks
|
Wistar, diabetic animal, STZ injection, left ventricle heart tissue, blood glucose level >15mM for the duration of the study
|
Gene expression data from LV heart tissue of diabetic animal 16wks after saline injection
|
| Sample_geo_accession | GSM130869
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Male wistars were anaesthetised (Halothane 2-5%) and received a tail vein injection of STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130869/suppl/GSM130869.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130870 | GPL1355 |
|
LVHeart_Diabetic648_16wks, biological rep4
|
Diabetic, left ventricle (LV) heart tissue, 16wks
|
Wistar, diabetic animal, STZ injection, left ventricle heart tissue, blood glucose level >15mM for the duration of the study
|
Gene expression data from LV heart tissue of diabetic animal 16wks after saline injection
|
| Sample_geo_accession | GSM130870
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Male wistars were anaesthetised (Halothane 2-5%) and received a tail vein injection of STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130870/suppl/GSM130870.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130871 | GPL1355 |
|
LVHeart_Diabetic968_16wks, biological rep5
|
Diabetic, left ventricle (LV) heart tissue, 16wks
|
Wistar, diabetic animal, STZ injection, left ventricle heart tissue, blood glucose level >15mM for the duration of the study
|
Gene expression data from LV heart tissue of diabetic animal 16wks after saline injection
|
| Sample_geo_accession | GSM130871
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Male wistars were anaesthetised (Halothane 2-5%) and received a tail vein injection of STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130871/suppl/GSM130871.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130872 | GPL1355 |
|
LVHeart_Diabetic226_16wks, biological rep6
|
Diabetic, left ventricle (LV) heart tissue, 16wks
|
Wistar, diabetic animal, STZ injection, left ventricle heart tissue, blood glucose level >15mM for the duration of the study
|
Gene expression data from LV heart tissue of diabetic animal 16wks after saline injection
|
| Sample_geo_accession | GSM130872
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Male wistars were anaesthetised (Halothane 2-5%) and received a tail vein injection of STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130872/suppl/GSM130872.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
|
GSM130873 | GPL1355 |
|
LVHeart_Diabetic465_16wks, biological rep7
|
Diabetic, left ventricle (LV) heart tissue, 16wks
|
Wistar, diabetic animal, STZ injection, left ventricle heart tissue, blood glucose level >15mM for the duration of the study
|
Gene expression data from LV heart tissue of diabetic animal 16wks after saline injection
|
| Sample_geo_accession | GSM130873
| | Sample_status | Public on Oct 31 2006
| | Sample_submission_date | Aug 25 2006
| | Sample_last_update_date | Oct 31 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | Whole heart was excised from animal after cervical dislocation and perfused with 60ml of DEPC treated PBS pH 7.4 at 15ml/min. LV was dissected away and stored in RNA later (Qiagen) at -80C
| | Sample_growth_protocol_ch1 | Male wistars were anaesthetised (Halothane 2-5%) and received a tail vein injection of STZ 60mg/kg. Animals were recovered and housed in pairs on fibrecycle bedding (12 hr light:dark cycle, 50-70 % humidity, 19-21 °C) for the duration of the study (16wks)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted using Qiagen Rneasy MIDI Total RNA extraction kit or Ambion Mini RNAqueous RNA extraction kit as per the manufacturers protocol
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 microg of cRNA were hybridized for 16 hr at 45C on GeneChip Rat 230 2.0 Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip® Scanner 3000
| | Sample_data_processing | This data was analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100. Additional data processing was performed using .CEL files for publication (manuscript in preparation). Briefly, all analyses were performed in R (Ihaka, 1996) using the Bioconductor collection of analysis packages (Gentleman, 2004). Normalization was by the Robust Multichip Averaging (RMA) algorithm of Irizzary et al., (Irizarry, 2003) as implemented in the Affy package for Bioconductor (Gautier, 2004 #238) without background correction. Probe sets undergoing changes in expression level were detected with the limma package (Smyth, 2005) with the moderated t-statistic of Smyth (Smyth, 2004) used to assess the strength of differential expression (relative to variability) for each probe set. Benjamini and Hochberg’s False Discovery Rate controlling method was used to produce adjusted P-values to limit the expected proportion of false positive results to < 5% (Benjamini, 1995).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Sarah,,Glyn-Jones
| | Sample_contact_email | s.glyn-jones@auckland.ac.nz
| | Sample_contact_laboratory | Proteomics and Biomedicine
| | Sample_contact_department | School of Biological Sciences
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 3A Symonds St
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1142
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM130nnn/GSM130873/suppl/GSM130873.CEL.gz
| | Sample_series_id | GSE5606
| | Sample_data_row_count | 31099
| | |
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