Search results for the GEO ID: GSE20967  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM524171 | GPL1355 |
|
one month old SD, biological rep1
|
retina of one month old SD
|
tissue: retina
strain: Sprague-Dawley
age: one month old
genotype: wild type
|
Gene expression data from retina of 1m old SD rat
|
| Sample_geo_accession | GSM524171
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524171/suppl/GSM524171_SD_1mo_1.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524172 | GPL1355 |
|
one month old SD, biological rep2
|
retina of one month old SD
|
tissue: retina
strain: Sprague-Dawley
age: one month old
genotype: wild type
|
Gene expression data from retina of 1m old SD rat
|
| Sample_geo_accession | GSM524172
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524172/suppl/GSM524172_SD_1mo_2.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524173 | GPL1355 |
|
one month old SD, biological rep3
|
retina of one month old SD
|
tissue: retina
strain: Sprague-Dawley
age: one month old
genotype: wild type
|
Gene expression data from retina of 1m old SD rat
|
| Sample_geo_accession | GSM524173
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524173/suppl/GSM524173_SD_1mo_3.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524174 | GPL1355 |
|
three month old SD, biological rep1
|
retina of three month old SD
|
tissue: retina
strain: Sprague-Dawley
age: three month old
genotype: wild type
|
Gene expression data from retina of 3m old SD rat
|
| Sample_geo_accession | GSM524174
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524174/suppl/GSM524174_SD_3mo_4.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524175 | GPL1355 |
|
three month old SD, biological rep2
|
retina of three month old SD
|
tissue: retina
strain: Sprague-Dawley
age: three month old
genotype: wild type
|
Gene expression data from retina of 3m old SD rat
|
| Sample_geo_accession | GSM524175
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524175/suppl/GSM524175_SD_3mo_5.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524176 | GPL1355 |
|
three month old SD, biological rep3
|
retina of three month old SD
|
tissue: retina
strain: Sprague-Dawley
age: three month old
genotype: wild type
|
Gene expression data from retina of 3m old SD rat
|
| Sample_geo_accession | GSM524176
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524176/suppl/GSM524176_SD_3mo_6.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524177 | GPL1355 |
|
one month old TGR, biological rep1
|
retina of one month old TGR
|
tissue: retina
strain: PKD-2-247
age: one month old
genotype: truncated polycystin-2
|
Gene expression data from retina of 1m old PKD rat
|
| Sample_geo_accession | GSM524177
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524177/suppl/GSM524177_PKD_1mo_7.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524178 | GPL1355 |
|
one month old TGR, biological rep2
|
retina of one month old TGR
|
tissue: retina
strain: PKD-2-247
age: one month old
genotype: truncated polycystin-2
|
Gene expression data from retina of 1m old PKD rat
|
| Sample_geo_accession | GSM524178
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524178/suppl/GSM524178_PKD_1mo_8.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524179 | GPL1355 |
|
one month old TGR, biological rep3
|
retina of one month old TGR
|
tissue: retina
strain: PKD-2-247
age: one month old
genotype: truncated polycystin-2
|
Gene expression data from retina of 1m old PKD rat
|
| Sample_geo_accession | GSM524179
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524179/suppl/GSM524179_PKD_1mo_9.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524180 | GPL1355 |
|
three month old TGR, biological rep1
|
retina of three month old TGR
|
tissue: retina
strain: PKD-2-247
age: three month old
genotype: truncated polycystin-2
|
Gene expression data from retina of 3m old PKD rat
|
| Sample_geo_accession | GSM524180
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524180/suppl/GSM524180_PKD_3mo_10.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524181 | GPL1355 |
|
three month old TGR, biological rep2
|
retina of three month old TGR
|
tissue: retina
strain: PKD-2-247
age: three month old
genotype: truncated polycystin-2
|
Gene expression data from retina of 3m old PKD rat
|
| Sample_geo_accession | GSM524181
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524181/suppl/GSM524181_PKD_3mo_11.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
|
GSM524182 | GPL1355 |
|
three month old TGR, biological rep3
|
retina of three month old TGR
|
tissue: retina
strain: PKD-2-247
age: three month old
genotype: truncated polycystin-2
|
Gene expression data from retina of 3m old PKD rat
|
| Sample_geo_accession | GSM524182
| | Sample_status | Public on Mar 15 2011
| | Sample_submission_date | Mar 19 2010
| | Sample_last_update_date | Mar 15 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Rattus norvegicus
| | Sample_taxid_ch1 | 10116
| | Sample_treatment_protocol_ch1 | The eyes frozen in –80°C were dissected under a microdissection microscope. The cornea, lens and vitreous were removed, and the retina was isolated from the choroids with scissors and tweezers. After dissection, the retinas were immediately transferred into a tube with Trizol as extraction reagent.
| | Sample_growth_protocol_ch1 | Male homozygous TGR and male SD rats were held in a 12 hours light and dark cycle with free access to food and drinking water. Generation and genotyping of the transgenic rats were described previously in the publication (A truncated polycystin-2 protein causes polycystic kidney disease and retinal degeneration in transgenic rats. Gallagher AR et al., J Am Soc Nephrol. 2006 Oct;17(10):2719-30). After sacrifice, the eyes from TGR and SD rats at 1 and 3 months were immediately frozen for quantitative extraction of RNA.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Retinal total RNA was individually extracted using Trizol reagent (Invitrogen, Germany) according to the manufacturer’s protocol.
| | 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 | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Rat Genome 230 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner3000.
| | Sample_data_processing | The data were quantile normalized and analyzed with GMP Genomics based on mixed model ANOVA.
| | Sample_platform_id | GPL1355
| | Sample_contact_name | Li,,Li
| | Sample_contact_email | li.li@gmx.de
| | Sample_contact_institute | University Heidelberg
| | Sample_contact_address | Theodor-Kutzer-Ufer
| | Sample_contact_city | Mannheim
| | Sample_contact_zip/postal_code | 68167
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM524nnn/GSM524182/suppl/GSM524182_PKD_3mo_12.CEL.gz
| | Sample_series_id | GSE20967
| | Sample_data_row_count | 31099
| | |
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