Search results for the GEO ID: GSE21448  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM536088 | GPL1261 |
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control sham
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pooled RNA from 4 FVB-sham mice
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strain/background: FVB/NJ
genotype: control
tissue: kidney
gender: female
age: 4.5 months
disease: nondiabetic
surgery: sham
time after surgery: 10 weeks
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FVB-sham: sham surgery treatment in nondiabetic mice.
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| Sample_geo_accession | GSM536088
| | Sample_status | Public on Apr 15 2011
| | Sample_submission_date | Apr 21 2010
| | Sample_last_update_date | Apr 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Uninephrectomy was applied to OVE26 mice and their littermates at the age of 2 months. All mice were sacrificed under anesthesia at 4.5 months of age, which was 10 weeks after surgery. Kidneys were harvested under anesthesia and perfused with phosphate-buffered saline. Half of the kidney from each animal was snap frozen in liquid nitrogen and stored at -80C for RNA extraction.
| | Sample_growth_protocol_ch1 | OVE diabetic mice on the FVB background were bred in our animal facility and had free access to standard rodent chow and water throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from frozen kidney using TriZol reagent. RNA was pooled from 4 mice in each group (OVE-uni, OVE-sham, FVB-uni, FVB-sham). A 100ng aliquot of RNA from the pooled sample was used for probe preparation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 3' IVT Express Kit was used for biotin labeling.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on a GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned using a GCS 3000 7G scanner and GCOS software (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | To identify genes altered by diabetes, two comparisons of signal intensity were made, OVE-uni versus FVB-uni (designated as UNI ratio) and OVE-sham versus FVB-sham (designated as SHAM ratio). The ratio of normalized signal intensity was determined for each probe set on the chip. Genes with a two-fold or greater change in signal were uploaded to Ingenuity software (Ingenuity Pathway Analysis, Redwood City, CA) for canonical pathway analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shirong,,Zheng
| | Sample_contact_email | zhengsr38@hotmail.com
| | Sample_contact_phone | 502-852-2632
| | Sample_contact_laboratory | Dr. Paul N Epstein
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University of Louisville
| | Sample_contact_address | 570 S Preston St.
| | Sample_contact_city | Louisville
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM536nnn/GSM536088/suppl/GSM536088.CEL.gz
| | Sample_series_id | GSE21448
| | Sample_data_row_count | 45101
| | |
|
GSM536089 | GPL1261 |
|
control uninephrectomy
|
pooled RNA from 4 FVB-uni mice
|
strain/background: FVB/NJ
genotype: control
tissue: kidney
gender: female
age: 4.5 months
disease: nondiabetic
surgery: uninephrectomy
time after surgery: 10 weeks
|
FVB-uni: uninephrectomy treatment in nondiabetic mice.
|
| Sample_geo_accession | GSM536089
| | Sample_status | Public on Apr 15 2011
| | Sample_submission_date | Apr 21 2010
| | Sample_last_update_date | Apr 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Uninephrectomy was applied to OVE26 mice and their littermates at the age of 2 months. All mice were sacrificed under anesthesia at 4.5 months of age, which was 10 weeks after surgery. Kidneys were harvested under anesthesia and perfused with phosphate-buffered saline. Half of the kidney from each animal was snap frozen in liquid nitrogen and stored at -80C for RNA extraction.
| | Sample_growth_protocol_ch1 | OVE diabetic mice on the FVB background were bred in our animal facility and had free access to standard rodent chow and water throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from frozen kidney using TriZol reagent. RNA was pooled from 4 mice in each group (OVE-uni, OVE-sham, FVB-uni, FVB-sham). A 100ng aliquot of RNA from the pooled sample was used for probe preparation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 3' IVT Express Kit was used for biotin labeling.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on a GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned using a GCS 3000 7G scanner and GCOS software (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | To identify genes altered by diabetes, two comparisons of signal intensity were made, OVE-uni versus FVB-uni (designated as UNI ratio) and OVE-sham versus FVB-sham (designated as SHAM ratio). The ratio of normalized signal intensity was determined for each probe set on the chip. Genes with a two-fold or greater change in signal were uploaded to Ingenuity software (Ingenuity Pathway Analysis, Redwood City, CA) for canonical pathway analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shirong,,Zheng
| | Sample_contact_email | zhengsr38@hotmail.com
| | Sample_contact_phone | 502-852-2632
| | Sample_contact_laboratory | Dr. Paul N Epstein
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University of Louisville
| | Sample_contact_address | 570 S Preston St.
| | Sample_contact_city | Louisville
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM536nnn/GSM536089/suppl/GSM536089.CEL.gz
| | Sample_series_id | GSE21448
| | Sample_data_row_count | 45101
| | |
|
GSM536090 | GPL1261 |
|
diabetes sham
|
pooled RNA from 4 OVE-sham mice
|
strain/background: FVB/NJ
genotype: OVE26 transgenic
tissue: kidney
gender: female
age: 4.5 months
disease: diabetic
surgery: sham
time after surgery: 10 weeks
|
OVE-sham: sham surgery treatment in diabetic mice.
|
| Sample_geo_accession | GSM536090
| | Sample_status | Public on Apr 15 2011
| | Sample_submission_date | Apr 21 2010
| | Sample_last_update_date | Apr 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Uninephrectomy was applied to OVE26 mice and their littermates at the age of 2 months. All mice were sacrificed under anesthesia at 4.5 months of age, which was 10 weeks after surgery. Kidneys were harvested under anesthesia and perfused with phosphate-buffered saline. Half of the kidney from each animal was snap frozen in liquid nitrogen and stored at -80C for RNA extraction.
| | Sample_growth_protocol_ch1 | OVE diabetic mice on the FVB background were bred in our animal facility and had free access to standard rodent chow and water throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from frozen kidney using TriZol reagent. RNA was pooled from 4 mice in each group (OVE-uni, OVE-sham, FVB-uni, FVB-sham). A 100ng aliquot of RNA from the pooled sample was used for probe preparation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 3' IVT Express Kit was used for biotin labeling.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on a GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned using a GCS 3000 7G scanner and GCOS software (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | To identify genes altered by diabetes, two comparisons of signal intensity were made, OVE-uni versus FVB-uni (designated as UNI ratio) and OVE-sham versus FVB-sham (designated as SHAM ratio). The ratio of normalized signal intensity was determined for each probe set on the chip. Genes with a two-fold or greater change in signal were uploaded to Ingenuity software (Ingenuity Pathway Analysis, Redwood City, CA) for canonical pathway analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shirong,,Zheng
| | Sample_contact_email | zhengsr38@hotmail.com
| | Sample_contact_phone | 502-852-2632
| | Sample_contact_laboratory | Dr. Paul N Epstein
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University of Louisville
| | Sample_contact_address | 570 S Preston St.
| | Sample_contact_city | Louisville
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM536nnn/GSM536090/suppl/GSM536090.CEL.gz
| | Sample_series_id | GSE21448
| | Sample_data_row_count | 45101
| | |
|
GSM536091 | GPL1261 |
|
diabetes uninephrectomy
|
pooled RNA from 4 OVE-uni mice
|
strain/background: FVB/NJ
genotype: OVE26 transgenic
tissue: kidney
gender: female
age: 4.5 months
disease: diabetic
surgery: uninephrectomy
time after surgery: 10 weeks
|
OVE-uni: uninephrectomy treatment in diabetic mice.
|
| Sample_geo_accession | GSM536091
| | Sample_status | Public on Apr 15 2011
| | Sample_submission_date | Apr 21 2010
| | Sample_last_update_date | Apr 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Uninephrectomy was applied to OVE26 mice and their littermates at the age of 2 months. All mice were sacrificed under anesthesia at 4.5 months of age, which was 10 weeks after surgery. Kidneys were harvested under anesthesia and perfused with phosphate-buffered saline. Half of the kidney from each animal was snap frozen in liquid nitrogen and stored at -80C for RNA extraction.
| | Sample_growth_protocol_ch1 | OVE diabetic mice on the FVB background were bred in our animal facility and had free access to standard rodent chow and water throughout the study.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted from frozen kidney using TriZol reagent. RNA was pooled from 4 mice in each group (OVE-uni, OVE-sham, FVB-uni, FVB-sham). A 100ng aliquot of RNA from the pooled sample was used for probe preparation.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 3' IVT Express Kit was used for biotin labeling.
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA was hybridized for 16 hr at 45C on a GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | Arrays were scanned using a GCS 3000 7G scanner and GCOS software (Affymetrix, Santa Clara, CA).
| | Sample_data_processing | To identify genes altered by diabetes, two comparisons of signal intensity were made, OVE-uni versus FVB-uni (designated as UNI ratio) and OVE-sham versus FVB-sham (designated as SHAM ratio). The ratio of normalized signal intensity was determined for each probe set on the chip. Genes with a two-fold or greater change in signal were uploaded to Ingenuity software (Ingenuity Pathway Analysis, Redwood City, CA) for canonical pathway analysis.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Shirong,,Zheng
| | Sample_contact_email | zhengsr38@hotmail.com
| | Sample_contact_phone | 502-852-2632
| | Sample_contact_laboratory | Dr. Paul N Epstein
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | University of Louisville
| | Sample_contact_address | 570 S Preston St.
| | Sample_contact_city | Louisville
| | Sample_contact_state | KY
| | Sample_contact_zip/postal_code | 40202
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM536nnn/GSM536091/suppl/GSM536091.CEL.gz
| | Sample_series_id | GSE21448
| | Sample_data_row_count | 45101
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