Search results for the GEO ID: GSE45250  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1099801 | GPL1355 |
|
rvpm high stretch high shortening rep1
|
right ventricular papillary muscle, high mean stretch, high cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 85
weight: 297
|
A1
|
| Sample_geo_accession | GSM1099801
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099801/suppl/GSM1099801_A1.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099802 | GPL1355 |
|
rvpm high stretch high shortening rep2
|
right ventricular papillary muscle, high mean stretch, high cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 78
weight: 279
|
A2
|
| Sample_geo_accession | GSM1099802
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099802/suppl/GSM1099802_A2.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099803 | GPL1355 |
|
rvpm high stretch high shortening rep3
|
right ventricular papillary muscle, high mean stretch, high cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 81
weight: 283
|
A3
|
| Sample_geo_accession | GSM1099803
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099803/suppl/GSM1099803_A3.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099804 | GPL1355 |
|
rvpm high stretch low shortening rep1
|
right ventricular papillary muscle, high mean stretch, low cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 72
weight: 270
|
B1
|
| Sample_geo_accession | GSM1099804
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099804/suppl/GSM1099804_B1.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099805 | GPL1355 |
|
rvpm high stretch low shortening rep2
|
right ventricular papillary muscle, high mean stretch, low cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 81
weight: 280
|
B2
|
| Sample_geo_accession | GSM1099805
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099805/suppl/GSM1099805_B2.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099806 | GPL1355 |
|
rvpm high stretch low shortening rep3
|
right ventricular papillary muscle, high mean stretch, low cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 81
weight: 272
|
B3
|
| Sample_geo_accession | GSM1099806
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099806/suppl/GSM1099806_B3.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099807 | GPL1355 |
|
rvpm low stretch low shortening rep1
|
right ventricular papillary muscle, low mean stretch, low cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 75
weight: 311
|
C1
|
| Sample_geo_accession | GSM1099807
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099807/suppl/GSM1099807_C1.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099808 | GPL1355 |
|
rvpm low stretch low shortening rep2
|
right ventricular papillary muscle, low mean stretch, low cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 75
weight: 318
|
C2
|
| Sample_geo_accession | GSM1099808
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099808/suppl/GSM1099808_C2.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099809 | GPL1355 |
|
rvpm low stretch low shortening rep3
|
right ventricular papillary muscle, low mean stretch, low cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 75
weight: 305
|
C3
|
| Sample_geo_accession | GSM1099809
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099809/suppl/GSM1099809_C3.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099810 | GPL1355 |
|
rvpm low stretch high shortening rep1
|
right ventricular papillary muscle, low mean stretch, high cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 84
weight: 279
|
D1
|
| Sample_geo_accession | GSM1099810
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099810/suppl/GSM1099810_D1.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099811 | GPL1355 |
|
rvpm low stretch high shortening rep2
|
right ventricular papillary muscle, low mean stretch, high cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 84
weight: 296
|
D2
|
| Sample_geo_accession | GSM1099811
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099811/suppl/GSM1099811_D2.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
GSM1099812 | GPL1355 |
|
rvpm low stretch high shortening rep3
|
right ventricular papillary muscle, low mean stretch, high cyclic shortening, 12hr
|
strain: LBNF1
gender: male
age: 75
weight: 267
|
D3
|
| Sample_geo_accession | GSM1099812
| | Sample_status | Public on Mar 19 2013
| | Sample_submission_date | Mar 18 2013
| | Sample_last_update_date | Mar 19 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | After 12 hours of mechanically controlled muscle culture, the electrical stimulus and mechanical shortening were terminated and each muscle was carefully removed from the culture system, placed into a pyrogen free tube, flash frozen in liquid nitrogen, and stored at -80°C until further processing.
| | Sample_growth_protocol_ch1 | Each muscle was dissected from the right ventricle of an adult male LBNF rat and carefully hung in a sterilized muscle culture bath. Each muscle was bathed in well oxygenated, supplemented Medium 199 and stimulated to contract with a 2-4V biopolar square wave at 1Hz. At the beginning of the 12 hour culture period, each muscle was incrementally stretched from slack to a pre-defined length to establish a baseline low or high mean stretch. A muscle-specific computer-generated waveform was then initiated to impose a low or high percentage of cyclic shortening, as defined by the mechanical group design. The culture media was maintainted at 37°C and exchanged for fresh media at the 6 hour time point. Mechanical stretch and shortening were monitored at 0, 3, 6, 9, and 12 hours to ensure accurate and precise mechanical control throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | While frozen in liquid nitrogen, each muscle was mechanically homogenized via pulverization with a pyrogen-free pestle with a hard polymeric head followed by Trizol incubation and mechanical shearing by drawing the Trizol-tissue cocktail through a 25 gauge needle three times. Glycogen was added to each sample, and Trizol extraction was conducted according to the manufacturer's instructions, including the addition of DNase I treatment. Each sample concentration was measured twice and DNAse free water added to ensure a 100 ng total RNA sample in total volume of 3μl.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA (3' IVT Express Kit User Manual, www.affymetrix.com).
| | Sample_hyb_protocol | Following fragmentation, cRNA were hybridized on GeneChip Rat Genome 230 2.0 Array. GeneChips were washed and stained per the appropriate Affymetrix user manual (3' IVT Express Kit User Manual).
| | Sample_scan_protocol | GeneChips were scanned per the appropriate Affymetrix user manual (Expression Wash, Stain and Scan User Manual for Cartridge Arrays, www.affymetrix.com).
| | Sample_data_processing | The CEL files for each of 12 microarrays were read into R using the Bioconductor ReadAffy function. The Robust Multichip Average (RMA) algorithm was then used within R to normalize expression values across all probesets and microarrays. Finally, the spike-in controls were removed from the raw dataset (reduced probesets from 31,099 to 31,042) and a script was written to remove probesets whose expression was very low across at least 2 microarrays in each of the four experimental groups (reduced probesets from 31,042 to 16,391). Specifically, if the log2-transformed expression for a probeset was less than log2(50) on at least two microarrays within one or more mechanical groups, the probeset was removed from additional analysis. The resulting log2-transformed expression values are included in the Matrix tab of this spreadsheet. Filtered results are provided as a supplementary file on the Series record.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Charles,,Haggart
| | Sample_contact_email | charles.haggart@gmail.com
| | Sample_contact_laboratory | Cardiac Biomechanics Group
| | Sample_contact_department | Biomedical Engineering
| | Sample_contact_institute | University of Virginia
| | Sample_contact_address | 415 Lane Road
| | Sample_contact_city | Charlottesville
| | Sample_contact_state | VA
| | Sample_contact_zip/postal_code | 22908
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1099nnn/GSM1099812/suppl/GSM1099812_D3.CEL.gz
| | Sample_series_id | GSE45250
| | Sample_data_row_count | 31099
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
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