Search results for the GEO ID: GSE20214  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM506944 | GPL1355 |
|
DR+/+ at day40, biological rep1
|
Diabetes inducible rats, no mutation at LYP locus
|
tissue: pancreatic islets
strain: DR strain (diabetes resistant, but inducible)
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506944
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506944/suppl/GSM506944_DR++_d40_rep1.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506945 | GPL1355 |
|
DR+/+ at day40, biological rep2
|
Diabetes inducible rats, no mutation at LYP locus
|
tissue: pancreatic islets
strain: DR strain (diabetes resistant, but inducible)
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506945
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506945/suppl/GSM506945_DR++_d40_rep2.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506946 | GPL1355 |
|
JB at day40, biological rep1
|
Diabetes inducible rats, no mutation at LYP locus
|
tissue: pancreatic islets
strain: JB strain (diabetes resistant, but inducible)
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506946
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506946/suppl/GSM506946_JB_d40_rep1.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506947 | GPL1355 |
|
JB at day40, biological rep2
|
Diabetes inducible rats, no mutation at LYP locus
|
tissue: pancreatic islets
strain: JB strain (diabetes resistant, but inducible)
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506947
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506947/suppl/GSM506947_JB_d40_rep2.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506948 | GPL1355 |
|
JBlyp/lyp at day40, biological rep1
|
Diabetes prone rats, with homozygous mutation at LYP locus
|
tissue: pancreatic islets
strain: Jblyp/lyp strain (diabetes prone)
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506948
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506948/suppl/GSM506948_JBlyp_d40_rep1.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506949 | GPL1355 |
|
JBlyp/lyp at day40, biological rep2
|
Diabetes prone rats, with homozygous mutation at LYP locus
|
tissue: pancreatic islets
strain: Jblyp/lyp strain (diabetes prone)
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506949
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506949/suppl/GSM506949_JBlyp_d40_rep2.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506950 | GPL1355 |
|
F344 at day40, biological rep1
|
Healthy control rats
|
tissue: pancreatic islets
strain: healthy F344 strain
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506950
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506950/suppl/GSM506950_F344_d40_rep1.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506951 | GPL1355 |
|
F344 at day40, biological rep2
|
Healthy control rats
|
tissue: pancreatic islets
strain: healthy F344 strain
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506951
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506951/suppl/GSM506951_F344_d40_rep2.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506952 | GPL1355 |
|
F344lyp at day40, biological rep1
|
Healthy control rats
|
tissue: pancreatic islets
strain: healthy F344lyp strain
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506952
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506952/suppl/GSM506952_F344lyp_d40_rep1.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
GSM506953 | GPL1355 |
|
F344lyp at day40, biological rep2
|
Healthy control rats
|
tissue: pancreatic islets
strain: healthy F344lyp strain
age: 40 days old
|
Gene expression interrogating 31099 transcripts
|
| Sample_geo_accession | GSM506953
| | Sample_status | Public on Feb 10 2010
| | Sample_submission_date | Feb 05 2010
| | Sample_last_update_date | Sep 08 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | When collecting tissues for histological studies and islet isolation, animals were fasted for 12 h, weighed, and had blood glucose levels measured with a Bayer Ascensia Elite XL glucometer. Animals possessing blood glucose levels above 250 mg/dl were disqualified. Animals were anesthetized under isoflourane during for collection of tissues for histological studies. When harvesting pancreata from islets of Langerhans isolated from day 40 WF, F344, F344lyp/lyp, DR+/+ and DRlyp/lyp rats for islet isolation, only male animals were used. Rats were anesthetized by intraperitoneal injection of sodium pentobarbital (0.15 mg/g) and islets were prepared and purified as described.
| | Sample_growth_protocol_ch1 | Congenic BB rats, F344 rats and F344lyp rats were maintained at the University of Washington Seattle and at the Medical College of Wisconsin. DR+/+ and JBlyp/lyp animals were generated through mating of DRlyp/+ breeder pairs and identified through genotyping of simple sequence repeat markers as previously described. WF rats were obtained from Harlan Teklad (Madison, WI) and allowed to acclimate onsite for 3–7 days prior to tissue collection. All institutional guidelines for the use and care of laboratory animals were reviewed by the University of Washington Seattle and Medical College of Wisconsin Institutional Animal Care and Use Committees (IACUC) and followed. All animals were kept under specific pathogen-free conditions with standard light/dark cycles and were fed a regular diet and water ad libitum.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Briefly, islets were prepared by injecting collagenase (10 ml of 0.23 mg/ml Liberase; Roche Molecular Biochemicals, Indianapolis, IN) into the pancreatic duct and surgically removing the pancreas. The pancreata were then placed into 15-ml conical tubes containing 5 ml of 0.23 mg/ml Liberase and incubated at 37°C for 30 min. The digestate was filtered, rinsed (Hank’s buffered salt solution), purified in a gradient solution of Optiprep (Nycomed, Oslo, Norway), and stabilized in Trizol. Total islet RNA was extracted using TRIzol reagent (Invitrogen Life Technologies)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Purified RNA (~50 ng) was amplified using an Affymetrix two-cycle cDNA synthesis kit (catalog no. 900432), and cRNA was synthesized, labeled, fragmented, and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. RNA from each culture was independently analyzed.
| | Sample_scan_protocol | After hybridization, arrays were washed, stained with PE-conjugated streptavidin (Molecular Probes), and scanned.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA; www.bioconductor.org/) to determine signal log ratios. The statistical significance of differential gene expression was derived through a Student’s t test and false discovery rates (FDR) were determined with Significance Analysis of Microarrays (SAM) software.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM506nnn/GSM506953/suppl/GSM506953_F344lyp_d40_rep2.CEL.gz
| | Sample_series_id | GSE20214
| | Sample_data_row_count | 31099
| | |
|
| |
| |
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