Search results for the GEO ID: GSE7869  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM190858 | GPL570 |
|
PKD1 renal cyst, small cyst_1, < 1ml
|
Renal cyst from PKD1 patient, pooled from 4 different small cysts
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190858
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190858/suppl/GSM190858.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190859 | GPL570 |
|
PKD1 renal cyst, small cyst_2, < 1ml
|
Renal cyst from PKD1 patient, pooled from 4 different small cysts
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190859
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190859/suppl/GSM190859.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190860 | GPL570 |
|
PKD1 renal cyst, small cyst_3, < 1ml
|
Renal cyst from PKD1 patient, pooled from 4 different small cysts
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190860
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190860/suppl/GSM190860.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190861 | GPL570 |
|
PKD1 renal cyst, small cyst_4, < 1ml
|
Renal cyst from PKD1 patient, pooled from 4 different small cysts
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190861
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190861/suppl/GSM190861.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190862 | GPL570 |
|
PKD1 renal cyst, small cyst_5, < 1ml
|
Renal cyst from PKD1 patient, pooled from 4 different small cysts
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190862
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190862/suppl/GSM190862.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190863 | GPL570 |
|
PKD1 renal cyst, medium cyst_1, 23 ml
|
Renal cyst from PKD1 patient, medium single cyst
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190863
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190863/suppl/GSM190863.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190864 | GPL570 |
|
PKD1 renal cyst, medium cyst_2, 20 ml
|
Renal cyst from PKD1 patient, medium single cyst
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190864
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190864/suppl/GSM190864.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190865 | GPL570 |
|
PKD1 renal cyst, medium cyst_3, 11 ml
|
Renal cyst from PKD1 patient, medium single cyst
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190865
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190865/suppl/GSM190865.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190866 | GPL570 |
|
PKD1 renal cyst, medium cyst_4, 15 ml
|
Renal cyst from PKD1 patient, medium single cyst
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190866
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190866/suppl/GSM190866.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190867 | GPL570 |
|
PKD1 renal cyst, medium cyst_5, 19 ml
|
Renal cyst from PKD1 patient, medium single cyst
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190867
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190867/suppl/GSM190867.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190868 | GPL570 |
|
PKD1 renal cyst, large cyst_1, 60 ml
|
Renal cyst from PKD1 patient, large single cyst
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190868
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190868/suppl/GSM190868.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190869 | GPL570 |
|
PKD1 renal cyst, large cyst_2, 50 ml
|
Renal cyst from PKD1 patient, large single cyst
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190869
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190869/suppl/GSM190869.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190870 | GPL570 |
|
PKD1 renal cyst, large cyst_3, 100 ml
|
Renal cyst from PKD1 patient, large single cyst
|
PKD1 patient
|
PKD1 renal cyst
|
| Sample_geo_accession | GSM190870
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190870/suppl/GSM190870.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190871 | GPL570 |
|
minimally cystic tissue_1
|
Minimally cystic tissue from PKD1 patient
|
PKD1 patient
|
PKD1 control tissue
|
| Sample_geo_accession | GSM190871
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190871/suppl/GSM190871.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190872 | GPL570 |
|
minimally cystic tissue_2
|
Minimally cystic tissue from PKD1 patient
|
PKD1 patient
|
PKD1 control tissue
|
| Sample_geo_accession | GSM190872
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190872/suppl/GSM190872.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190873 | GPL570 |
|
minimally cystic tissue_3
|
Minimally cystic tissue from PKD1 patient
|
PKD1 patient
|
PKD1 control tissue
|
| Sample_geo_accession | GSM190873
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190873/suppl/GSM190873.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190874 | GPL570 |
|
minimally cystic tissue_4
|
Minimally cystic tissue from PKD1 patient
|
PKD1 patient
|
PKD1 control tissue
|
| Sample_geo_accession | GSM190874
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190874/suppl/GSM190874.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190875 | GPL570 |
|
minimally cystic tissue_5
|
Minimally cystic tissue from PKD1 patient
|
PKD1 patient
|
PKD1 control tissue
|
| Sample_geo_accession | GSM190875
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190875/suppl/GSM190875.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190876 | GPL570 |
|
normal renal cortical tissue_1
|
Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 1
|
PKD1 patient
|
normal control tissue
|
| Sample_geo_accession | GSM190876
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190876/suppl/GSM190876.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190877 | GPL570 |
|
normal renal cortical tissue_2
|
Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 2
|
PKD1 patient
|
normal control tissue
|
| Sample_geo_accession | GSM190877
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190877/suppl/GSM190877.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
|
GSM190878 | GPL570 |
|
normal renal cortical tissue_3
|
Non-cancerous renal cortical tissue from nephrectomized kidney with isolated renal cell carcinoma of patient 3
|
PKD1 patient
|
normal control tissue
|
| Sample_geo_accession | GSM190878
| | Sample_status | Public on Aug 14 2009
| | Sample_submission_date | May 22 2007
| | Sample_last_update_date | Aug 14 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | All tissues were dissected within 30 minutes of nephrectomy, washed in cold phosphate-buffered saline, snapped frozen in liquid nitrogen, and stored in a -80o C freezer
| | Sample_growth_protocol_ch1 | The nephrectomized kidneys were kept cooled on ice immediately after their removal in the operating room and through out the tissue retrieval procedure in the surgical pathology suite, where the renal capsule was striped and individual cysts identified.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted from each sample using Absolutely RNA RT-PCR Miniprep Kit (Stratagene) with an on-column DNA digestion step to minimize genomic DNA contamination. The integrity of the RNA was assessed using the RNA 6000 Nano Assay on 2100 Bioanalyzer (Agilent Technologies) to ensure that the ratio of 28S to 18S rRNA was at least 2.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA samples were prepared according to the Affymetrix Two-Cycle Target Labeling Reagents for small sample from 50-100 ng total RNA.
| | Sample_hyb_protocol | Standard Affymetrix procedures, following fragmentation, 15 µg cRNA were hybridized for 16 hr at 45°C on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.
| | Sample_scan_protocol | Standard Affymetrix procedures by using the Affymetrix GeneArray Scanner 3000.
| | Sample_data_processing | Scanned raw data images and detection p-value were processed with GeneChip Operating Software (GCOS) 1.4. Probe set signal intensities were extracted and normalized by the Robust Multi-array Average (RMA) algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | York,PC,Pei
| | Sample_contact_email | york.pei@uhn.on.ca
| | Sample_contact_phone | 416-340-4257
| | Sample_contact_fax | 416-340-4999
| | Sample_contact_department | Department of Medicine
| | Sample_contact_institute | University of Toronto
| | Sample_contact_address | 8N838, 585 University Avenue
| | Sample_contact_city | Toronto
| | Sample_contact_state | Ontario
| | Sample_contact_zip/postal_code | M5G2N2
| | Sample_contact_country | Canada
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM190nnn/GSM190878/suppl/GSM190878.CEL.gz
| | Sample_series_id | GSE7869
| | Sample_data_row_count | 54675
| | |
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