Search results for the GEO ID: GSE20538 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM516173 | GPL570 |
|
fibroblast C1-0
|
control C1 fibroblasts, cultured with 0 nM T3
|
cell type: skin fibroblasts
condition: normal
|
Gene expression from controls cultured with 0 nM T3
|
Sample_geo_accession | GSM516173
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516173/suppl/GSM516173.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516174 | GPL570 |
|
fibroblast C1-1
|
control C1 fibroblasts, cultured with 1 nM T3
|
cell type: skin fibroblasts
condition: normal
|
Gene expression from controls cultured with 1 nM T3
|
Sample_geo_accession | GSM516174
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516174/suppl/GSM516174.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516175 | GPL570 |
|
fibroblast C1-10
|
control C1 fibroblasts, cultured with 10 nM T3
|
cell type: skin fibroblasts
condition: normal
|
Gene expression from controls cultured with 10 nM T3
|
Sample_geo_accession | GSM516175
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516175/suppl/GSM516175.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516176 | GPL570 |
|
fibroblast C2-0
|
control C2 fibroblasts, cultured with 0 nM T3
|
cell type: skin fibroblasts
condition: normal
|
Gene expression from controls cultured with 0 nM T3
|
Sample_geo_accession | GSM516176
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516176/suppl/GSM516176.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516177 | GPL570 |
|
fibroblast C2-10
|
control C2 fibroblasts, cultured with 10 nM T3
|
cell type: skin fibroblasts
condition: normal
|
Gene expression from controls cultured with 10 nM T3
|
Sample_geo_accession | GSM516177
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516177/suppl/GSM516177.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516178 | GPL570 |
|
fibroblast C3-0
|
control C3 fibroblasts, cultured with 0 nM T3
|
cell type: skin fibroblasts
condition: normal
|
Gene expression from controls cultured with 0 nM T3
|
Sample_geo_accession | GSM516178
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516178/suppl/GSM516178.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516179 | GPL570 |
|
fibroblast C3-1
|
control C3 fibroblasts, cultured with 1 nM T3
|
cell type: skin fibroblasts
condition: normal
|
Gene expression from controls cultured with 1 nM T3
|
Sample_geo_accession | GSM516179
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516179/suppl/GSM516179.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516180 | GPL570 |
|
fibroblast C3-10
|
control C3 fibroblasts, cultured with 10 nM T3
|
cell type: skin fibroblasts
condition: normal
|
Gene expression from controls cultured with 10 nM T3
|
Sample_geo_accession | GSM516180
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516180/suppl/GSM516180.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516181 | GPL570 |
|
fibroblast P1-0
|
patient P1 fibroblasts, cultured with 0 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 0 nM T3
|
Sample_geo_accession | GSM516181
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516181/suppl/GSM516181.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516182 | GPL570 |
|
fibroblast P1-1
|
patient P1 fibroblasts, cultured with 1 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 1 nM T3
|
Sample_geo_accession | GSM516182
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516182/suppl/GSM516182.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516183 | GPL570 |
|
fibroblast P1-10
|
patient P1 fibroblasts, cultured with 10 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 10 nM T3
|
Sample_geo_accession | GSM516183
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516183/suppl/GSM516183.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516184 | GPL570 |
|
fibroblast P2-0
|
patient P2 fibroblasts, cultured with 0 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 0 nM T3
|
Sample_geo_accession | GSM516184
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516184/suppl/GSM516184.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516185 | GPL570 |
|
fibroblast P2-1
|
patient P2 fibroblasts, cultured with 1 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 1 nM T3
|
Sample_geo_accession | GSM516185
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516185/suppl/GSM516185.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516186 | GPL570 |
|
fibroblast P2-10
|
patient P2 fibroblasts, cultured with 10 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 10 nM T3
|
Sample_geo_accession | GSM516186
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516186/suppl/GSM516186.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516187 | GPL570 |
|
fibroblast P3-0
|
patient P3 fibroblasts, cultured with 0 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 0 nM T3
|
Sample_geo_accession | GSM516187
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516187/suppl/GSM516187.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516188 | GPL570 |
|
fibroblast P3-1
|
patient P3 fibroblasts, cultured with 1 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 1 nM T3
|
Sample_geo_accession | GSM516188
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516188/suppl/GSM516188.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516189 | GPL570 |
|
fibroblast P3-10
|
patient P3 fibroblasts, cultured with 10 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 10 nM T3
|
Sample_geo_accession | GSM516189
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516189/suppl/GSM516189.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516190 | GPL570 |
|
fibroblast P4-0
|
patient P4 fibroblasts, cultured with 0 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 0 nM T3
|
Sample_geo_accession | GSM516190
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516190/suppl/GSM516190.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516191 | GPL570 |
|
fibroblast P4-1
|
patient P4 fibroblasts, cultured with 1 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 1 nM T3
|
Sample_geo_accession | GSM516191
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516191/suppl/GSM516191.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
GSM516192 | GPL570 |
|
fibroblast P4-10
|
patient P4 fibroblasts, cultured with 10 nM T3
|
cell type: skin fibroblasts
condition: MCT8 mutation
|
Gene expression from patients cultured with 10 nM T3
|
Sample_geo_accession | GSM516192
| Sample_status | Public on Aug 23 2010
| Sample_submission_date | Feb 26 2010
| Sample_last_update_date | Aug 23 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Fibroblasts were cultured for 24 h in medium containing 9% charcoal-treated FCS. After 24 h, medium was refreshed with the same medium containing 0,1 or 10 nM T3 for 24 h.
| Sample_growth_protocol_ch1 | Fibroblasts were cultured in DMEM/F12 medium supplemented with 9% FCS
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions and further purified by the RNeasy kit.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 3-5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45C on GeneChip U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | The data were scanned with a Affymetrix scanner and GCOS 1.4 was used for image processing
| Sample_data_processing | Raw intensities values of all samples were normalized by RMA normalization (Robust Multichip Analysis) (background correction and quantile normalization) using Partek version 6.4 (Partek Inc., St. Louis, MO). To visualize the clustering of the samples, PCA (Principal Component Analysis) was used. The normalized datafile was transposed and imported into OmniViz version 6.0.1 (Biowisdom, Ltd., Cambridge, UK) for further analysis.
| Sample_platform_id | GPL570
| Sample_contact_name | W,Edward,Visser
| Sample_contact_email | w.e.visser@erasmusmc.nl
| Sample_contact_phone | 0031107043415
| Sample_contact_laboratory | Thyroid lab
| Sample_contact_department | Internal Medicine
| Sample_contact_institute | Erasmus Medical Center
| Sample_contact_address | Dr Molewaterplein 50
| Sample_contact_city | Rotterdam
| Sample_contact_zip/postal_code | 3015 GE
| Sample_contact_country | Netherlands
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM516nnn/GSM516192/suppl/GSM516192.CEL.gz
| Sample_series_id | GSE20538
| Sample_data_row_count | 54675
| |
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
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Select GSMs and click on "Add groups" |
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