Search results for the GEO ID: GSE15074  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM377146 | GPL1355 |
|
Day 1 T Cells Cyclosporin
|
Day 1 T Cells Cyclosporin
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377146
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377146/suppl/GSM377146.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377147 | GPL1355 |
|
Day 3 T Cells Cyclosporin
|
Day 3 T Cells Cyclosporin
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377147
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377147/suppl/GSM377147.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377148 | GPL1355 |
|
Day 7 T Cells Cyclosporin
|
Day 7 T Cells Cyclosporin
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377148
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377148/suppl/GSM377148.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377149 | GPL1355 |
|
Day 1 heart Cyclosporin
|
Day 1 heart Cyclosporin
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377149
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377149/suppl/GSM377149.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377150 | GPL1355 |
|
Day 3 heart Cyclosporin
|
Day 3 heart Cyclosporin
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377150
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377150/suppl/GSM377150.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377151 | GPL1355 |
|
Day 7 heart Cyclosporin
|
Day 7 heart Cyclosporin
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377151
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377151/suppl/GSM377151.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377152 | GPL1355 |
|
Day 1 T Cells Cyc + peptide
|
Day 1 T Cells Cyc + peptide
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377152
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377152/suppl/GSM377152.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377153 | GPL1355 |
|
Day 3 T Cells Cyc + peptide
|
Day 3 T Cells Cyc + peptide
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377153
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377153/suppl/GSM377153.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377154 | GPL1355 |
|
Day 7 T Cells Cyc + peptide
|
Day 7 T Cells Cyc + peptide
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377154
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377154/suppl/GSM377154.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377155 | GPL1355 |
|
Day 1 heart Cyc + peptide
|
Day 1 heart Cyc + peptide
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377155
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377155/suppl/GSM377155.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377156 | GPL1355 |
|
Day 3 heart Cyc + pepetide
|
Day 3 heart Cyc + pepetide
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377156
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377156/suppl/GSM377156.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377157 | GPL1355 |
|
Day 7 heart Cyc + peptide
|
Day 7 heart Cyc + peptide
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377157
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377157/suppl/GSM377157.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377158 | GPL1355 |
|
Day 1 T Cells control
|
Day 1 T Cells control
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377158
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377158/suppl/GSM377158.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377159 | GPL1355 |
|
Day 3 T Cells control
|
Day 3 T Cells control
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377159
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377159/suppl/GSM377159.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377160 | GPL1355 |
|
Day 7 T Cells control
|
Day 7 T Cells control
|
cell type: T cell
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377160
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377160/suppl/GSM377160.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377161 | GPL1355 |
|
Day 1 heart control
|
Day 1 heart control
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377161
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377161/suppl/GSM377161.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377162 | GPL1355 |
|
Day 3 heart control
|
Day 3 heart control
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377162
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377162/suppl/GSM377162.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
GSM377163 | GPL1355 |
|
Day 7 heart control
|
Day 7 heart control
|
tissue: heart
gender: male
strain: Wistar Furth
|
n/a
|
| Sample_geo_accession | GSM377163
| | Sample_status | Public on Nov 11 2009
| | Sample_submission_date | Mar 03 2009
| | Sample_last_update_date | Nov 11 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | There were three experimental groups: 1. Transplantation control group without any treatment, 2. Transplantation in the presence of sub-therapeutic dose of CsA (acute rejection) which consisted of 3 day course of oral cyclosporine delivered by gavage feed (CsA, 10 mg/kg/day; day 0–2). Transplantation in the presence of sub-therapeutic dose of CsA supplemented with allochimeric molecule (CsA + peptide). Allochimeric peptide [a1h1/u]-RT1.Aa (GenWay, San Diego CA; 1mg/kg) was delivered through the portal vein into ACI recipients of WF hearts at the time of transplantation in addition to a 3 days course of oral cyclosporine delivered by gavage feed (CsA, 10mg/kg/day; day 0–2).
| | Sample_growth_protocol_ch1 | Adult male inbred Wistar Furth (WF; RT1.Au) and ACI (RT1.Aa) rats (180–250 gm) were purchased from Harlan Sprague Dawely (Indianapolis, IN). Heterotopic cardiac transplants were placed intra-abdominally.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Allografts were harvested at 1, 3 and 7 days post-transplantation, immediately placed in RNA Later (Applied Biosystems/Ambion, Austin, TX) and cut into< 0.5 cm pieces. After overnight infiltration at 40C they were kept in RNA Later at -700C until the isolation of total RNA. Heart samples were pulverized using a FreezerMill (SPEX CertiPrep, Edison, NJ) and then an aliquot of the pulverized tissue was homogenized using a TissueLyser (Qiagen, Valencia, CA). Total RNA was isolated from the homogenized sample using the RNeasy Fibrous Tissue Mini Kit (Qiagen, Valencia, CA) according to the manufacturer’s recommended protocol. The quantity and purity of the extracted RNA was evaluated using a NanoDrop ND-1000 spectrophotometer (Nanodrop Technologies, Wilmington, DE) and its integrity measured using an Agilent Bioanalyzer (Agilent Technologies, Palo Alto, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA samples were prepared according to the standard Enzo BioarrayTM protocol (Enzo Life Sciences). In brief, one ug of total RNA from each sample was converted to double-stranded cDNA with the BioarrayTM Single-Round RNA Amplification and Labeling Kit (Enzo Life Sciences). After second-strand synthesis, the cDNA was purified with the cDNA Purification Kit (Enzo Life Sciences). The resulting double-stranded DNA was then used to generate multiple copies of biotinylated cRNA by in vitro transcription with the BioarrayTM HighYieldTM RNA Transcript Labeling Kit (Enzo Life Sciences).
| | Sample_hyb_protocol | For each sample, 10 ug of biotinylated cRNA spiked with bioB, bioC, bioD and cre (Hybridization Control) was hybridized to an Affymetrix Rat 230 2.0 Microarray for 16 hours at 45ºC. Following hybridization, all arrays were washed and stained in an Affymetrix GeneChip Fluidics Station.
| | Sample_scan_protocol | Stained arrays were scanned with an Affymetrix GeneChip® Scanner 3000. Quality checks and data analyses were carried out using Affymetrix GeneChip Operating Software (GCOS) and Expression Console.
| | Sample_data_processing | The processed image file of the Affymetrix Rat 230 2.0 array contains over 31,000 probe sets representing approximately 28,700 well-substantiated rat genes (Affymetrix; www.affymetrix.com).
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Malgorzata,,Kloc
| | Sample_contact_email | mkloc@tmhs.org
| | Sample_contact_phone | 713-441-6875
| | Sample_contact_laboratory | Immuno Biology
| | Sample_contact_department | Surgery
| | Sample_contact_institute | The Methodist Hospital
| | Sample_contact_address | 6565 Fannin Street
| | Sample_contact_city | Houston
| | Sample_contact_state | TX
| | Sample_contact_zip/postal_code | 77030
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM377nnn/GSM377163/suppl/GSM377163.CEL.gz
| | Sample_series_id | GSE15074
| | Sample_data_row_count | 31099
| | |
|
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| |
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