Search results for the GEO ID: GSE5563  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM129237 | GPL570 |
|
con_B004
|
vulva biopsy of normal tissue
|
Gender: female, Age: 33 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129237
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129237/suppl/GSM129237.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129238 | GPL570 |
|
VIN_B017
|
vulva biopsy of vulvar intraepithelial neoplasia (VIN)
|
Gender: female, Age: 39 years, Tissue: VIN 3
|
Gene expression data of vulvar intraepithelial neoplasia (VIN)
|
| Sample_geo_accession | GSM129238
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129238/suppl/GSM129238.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129239 | GPL570 |
|
VIN_B027
|
vulva biopsy of vulvar intraepithelial neoplasia (VIN)
|
Gender: female, Age: 33 years, Tissue: VIN 3
|
Gene expression data of vulvar intraepithelial neoplasia (VIN)
|
| Sample_geo_accession | GSM129239
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129239/suppl/GSM129239.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129240 | GPL570 |
|
VIN_B040
|
vulva biopsy of vulvar intraepithelial neoplasia (VIN)
|
Gender: female, Age: 35 years, Tissue: VIN 3
|
Gene expression data of vulvar intraepithelial neoplasia (VIN)
|
| Sample_geo_accession | GSM129240
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129240/suppl/GSM129240.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129241 | GPL570 |
|
con_B043
|
vulva biopsy of normal tissue
|
Gender: female, Age: 54 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129241
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129241/suppl/GSM129241.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129242 | GPL570 |
|
VIN_B060
|
vulva biopsy of vulvar intraepithelial neoplasia (VIN)
|
Gender: female, Age: 45 years, Tissue: VIN 3
|
Gene expression data of vulvar intraepithelial neoplasia (VIN)
|
| Sample_geo_accession | GSM129242
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129242/suppl/GSM129242.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129244 | GPL570 |
|
con_B084
|
vulva biopsy of normal tissue
|
Gender: female, Age: 23 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129244
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129244/suppl/GSM129244.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129245 | GPL570 |
|
VIN_B090
|
vulva biopsy of vulvar intraepithelial neoplasia (VIN)
|
Gender: female, Age: 48 years, Tissue: VIN 3
|
Gene expression data of vulvar intraepithelial neoplasia (VIN)
|
| Sample_geo_accession | GSM129245
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129245/suppl/GSM129245.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129246 | GPL570 |
|
VIN_B105
|
vulva biopsy of vulvar intraepithelial neoplasia (VIN)
|
Gender: female, Age: 44 years, Tissue: VIN 3
|
Gene expression data of vulvar intraepithelial neoplasia (VIN)
|
| Sample_geo_accession | GSM129246
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129246/suppl/GSM129246.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129247 | GPL570 |
|
VIN_B109
|
vulva biopsy of vulvar intraepithelial neoplasia (VIN)
|
Gender: female, Age: 39 years, Tissue: VIN 3
|
Gene expression data of vulvar intraepithelial neoplasia (VIN)
|
| Sample_geo_accession | GSM129247
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129247/suppl/GSM129247.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129248 | GPL570 |
|
VIN_B116
|
vulva biopsy of vulvar intraepithelial neoplasia (VIN)
|
Gender: female, Age: 36 years, Tissue: VIN 3
|
Gene expression data of vulvar intraepithelial neoplasia (VIN)
|
| Sample_geo_accession | GSM129248
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129248/suppl/GSM129248.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129249 | GPL570 |
|
con_B124
|
vulva biopsy of normal tissue
|
Gender: female, Age: 16 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129249
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129249/suppl/GSM129249.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129250 | GPL570 |
|
con_B130
|
vulva biopsy of normal tissue
|
Gender: female, Age: 37 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129250
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129250/suppl/GSM129250.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129251 | GPL570 |
|
con_B131
|
vulva biopsy of normal tissue
|
Gender: female, Age: 38 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129251
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129251/suppl/GSM129251.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129252 | GPL570 |
|
con_B132
|
vulva biopsy of normal tissue
|
Gender: female, Age: 54 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129252
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129252/suppl/GSM129252.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129253 | GPL570 |
|
con_B135
|
vulva biopsy of normal tissue
|
Gender: female, Age: 43 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129253
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129253/suppl/GSM129253.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
GSM129254 | GPL570 |
|
con_B148
|
vulva biopsy of normal tissue
|
Gender: female, Age: 43 years, Tissue: normal vulva,
|
Gene expression data of normal vulvar tissue
|
| Sample_geo_accession | GSM129254
| | Sample_status | Public on Nov 01 2006
| | Sample_submission_date | Aug 18 2006
| | Sample_last_update_date | Aug 18 2006
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cryostat sections of vulvar biopsies were homogenized by sonography and RNA was isolated using Trizol (Invitrogen, Life Technologies, Philadelphia, PA, USA). 1 ?g of total RNA was used to prepare antisense biotinylated RNA (www.affymetrix.com). The level and quality of cRNA was measured on the Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA, USA) and only intact RNA was used. The cRNA was fragmented with the GeneChip Sample Cleanup Module (Affymetrix, Santa Clara, CA, USA). Hybridization to Affymetrix U133plus2 GeneChips (54,614 probe sets, representing approximately 47,000 transcripts), staining, washing, and scanning procedures were carried out as described (Affymetrix, Santa Clara).
| | Sample_growth_protocol_ch1 | not applicable
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions (Affymetrix, Santa Clara, CA, USA)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Hybridization to Affymetrix U133plus2 GeneChips , staining and washing were carried out as described (Affymetrix, Santa Clara).
| | Sample_scan_protocol | Scanning procedures were carried out as described by Affymetrix, Santa Clara.
| | Sample_data_processing | The data were analyzed with MRAExpress using Affymetrix default settings and were normalized according to the quantile method (Bolstad BM, Irizarry RA, Astrand M, Speed TP. A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics 2003;19:185-93). After normalization, the intensity values below 30 were set at 30.T
| | Sample_platform_id | GPL570
| | Sample_contact_name | Lindy,,Santegoets
| | Sample_contact_department | Obstetrics & Gynecology
| | Sample_contact_institute | Erasmus University Medical Center Rotterdam
| | Sample_contact_address | P.O. Box 2040
| | Sample_contact_city | Rotterdam
| | Sample_contact_zip/postal_code | 3000 CA
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM129nnn/GSM129254/suppl/GSM129254.CEL.gz
| | Sample_series_id | GSE5563
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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