Search results for the GEO ID: GSE17114  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM428037 | GPL570 |
|
PBMCs_BD_1
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: female
age at examination: 29
geographical origin: Aveiro
immunosuppressors: yes
|
scan date 1
|
| Sample_geo_accession | GSM428037
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428037/suppl/GSM428037.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428038 | GPL570 |
|
PBMCs_BD_2
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: female
age at examination: 40
geographical origin: Aveiro
immunosuppressors: yes
|
scan date 1
|
| Sample_geo_accession | GSM428038
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428038/suppl/GSM428038.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428039 | GPL570 |
|
PBMCs_BD_3
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: female
age at examination: 36
geographical origin: Aveiro
immunosuppressors: no
|
scan date 1
|
| Sample_geo_accession | GSM428039
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428039/suppl/GSM428039.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428040 | GPL570 |
|
PBMCs_BD_4
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: female
age at examination: 29
geographical origin: Aveiro
immunosuppressors: no
|
scan date 2
|
| Sample_geo_accession | GSM428040
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428040/suppl/GSM428040.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428041 | GPL570 |
|
PBMCs_BD_5
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: female
age at examination: 55
geographical origin: Guarda
immunosuppressors: no
|
scan date 3
|
| Sample_geo_accession | GSM428041
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428041/suppl/GSM428041.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428042 | GPL570 |
|
PBMCs_BD_6
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: female
age at examination: 30
geographical origin: Guarda
immunosuppressors: yes
|
scan date 2
|
| Sample_geo_accession | GSM428042
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428042/suppl/GSM428042.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428043 | GPL570 |
|
PBMCs_BD_7
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: female
age at examination: 44
geographical origin: Lisbon
immunosuppressors: yes
|
scan date 3
|
| Sample_geo_accession | GSM428043
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428043/suppl/GSM428043.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428044 | GPL570 |
|
PBMCs_BD_8
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: female
age at examination: 46
geographical origin: Lisbon
immunosuppressors: no
|
scan date 4
|
| Sample_geo_accession | GSM428044
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428044/suppl/GSM428044.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428045 | GPL570 |
|
PBMCs_BD_9
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: male
age at examination: 20
geographical origin: Aveiro
immunosuppressors: yes
|
scan date 1
|
| Sample_geo_accession | GSM428045
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428045/suppl/GSM428045.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428046 | GPL570 |
|
PBMCs_BD_10
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: male
age at examination: 57
geographical origin: Lisbon
immunosuppressors: no
|
scan date 2
|
| Sample_geo_accession | GSM428046
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428046/suppl/GSM428046.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428047 | GPL570 |
|
PBMCs_BD_11
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: male
age at examination: 50
geographical origin: Lisbon
immunosuppressors: yes
|
scan date 4
|
| Sample_geo_accession | GSM428047
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428047/suppl/GSM428047.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428048 | GPL570 |
|
PBMCs_BD_12
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: male
age at examination: 30
geographical origin: Lisbon
immunosuppressors: yes
|
scan date 4
|
| Sample_geo_accession | GSM428048
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428048/suppl/GSM428048.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428049 | GPL570 |
|
PBMCs_BD_13
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: male
age at examination: 33
geographical origin: Lisbon
immunosuppressors: yes
|
scan date 2
|
| Sample_geo_accession | GSM428049
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428049/suppl/GSM428049.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428050 | GPL570 |
|
PBMCs_BD_14
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: male
age at examination: 29
geographical origin: Lisbon
immunosuppressors: no
|
scan date 3
|
| Sample_geo_accession | GSM428050
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428050/suppl/GSM428050.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428051 | GPL570 |
|
PBMCs_BD_15
|
peripheral blood mononuclear cells
|
affected status: BD patient
gender: male
age at examination: 28
geographical origin: Lisbon
immunosuppressors: yes
|
scan date 3
|
| Sample_geo_accession | GSM428051
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428051/suppl/GSM428051.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428052 | GPL570 |
|
PBMCs_Control_1
|
peripheral blood mononuclear cells
|
affected status: control
gender: female
age at examination: 27
geographical origin: Aveiro
immunosuppressors: no
|
scan date 1
|
| Sample_geo_accession | GSM428052
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428052/suppl/GSM428052.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428053 | GPL570 |
|
PBMCs_Control_2
|
peripheral blood mononuclear cells
|
affected status: control
gender: female
age at examination: 32
geographical origin: Guarda
immunosuppressors: no
|
scan date 2
|
| Sample_geo_accession | GSM428053
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428053/suppl/GSM428053.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428054 | GPL570 |
|
PBMCs_Control_3
|
peripheral blood mononuclear cells
|
affected status: control
gender: female
age at examination: 62
geographical origin: Lisbon
immunosuppressors: no
|
scan date 3
|
| Sample_geo_accession | GSM428054
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428054/suppl/GSM428054.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428055 | GPL570 |
|
PBMCs_Control_4
|
peripheral blood mononuclear cells
|
affected status: control
gender: female
age at examination: 51
geographical origin: Lisbon
immunosuppressors: no
|
scan date 2
|
| Sample_geo_accession | GSM428055
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428055/suppl/GSM428055.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428056 | GPL570 |
|
PBMCs_Control_5
|
peripheral blood mononuclear cells
|
affected status: control
gender: female
age at examination: 26
geographical origin: Lisbon
immunosuppressors: no
|
scan date 4
|
| Sample_geo_accession | GSM428056
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428056/suppl/GSM428056.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428057 | GPL570 |
|
PBMCs_Control_6
|
peripheral blood mononuclear cells
|
affected status: control
gender: female
age at examination: 26
geographical origin: Lisbon
immunosuppressors: no
|
scan date 4
|
| Sample_geo_accession | GSM428057
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428057/suppl/GSM428057.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428058 | GPL570 |
|
PBMCs_Control_7
|
peripheral blood mononuclear cells
|
affected status: control
gender: female
age at examination: 46
geographical origin: Lisbon
immunosuppressors: no
|
scan date 4
|
| Sample_geo_accession | GSM428058
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428058/suppl/GSM428058.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428059 | GPL570 |
|
PBMCs_Control_8
|
peripheral blood mononuclear cells
|
affected status: control
gender: male
age at examination: 35
geographical origin: Aveiro
immunosuppressors: no
|
scan date 1
|
| Sample_geo_accession | GSM428059
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428059/suppl/GSM428059.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428060 | GPL570 |
|
PBMCs_Control_9
|
peripheral blood mononuclear cells
|
affected status: control
gender: male
age at examination: 42
geographical origin: Aveiro
immunosuppressors: no
|
scan date 4
|
| Sample_geo_accession | GSM428060
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428060/suppl/GSM428060.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428061 | GPL570 |
|
PBMCs_Control_10
|
peripheral blood mononuclear cells
|
affected status: control
gender: male
age at examination: 31
geographical origin: Aveiro
immunosuppressors: no
|
scan date 4
|
| Sample_geo_accession | GSM428061
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428061/suppl/GSM428061.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428062 | GPL570 |
|
PBMCs_Control_11
|
peripheral blood mononuclear cells
|
affected status: control
gender: male
age at examination: 28
geographical origin: Aveiro
immunosuppressors: no
|
scan date 3
|
| Sample_geo_accession | GSM428062
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428062/suppl/GSM428062.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428063 | GPL570 |
|
PBMCs_Control_12
|
peripheral blood mononuclear cells
|
affected status: control
gender: male
age at examination: 61
geographical origin: Guarda
immunosuppressors: no
|
scan date 3
|
| Sample_geo_accession | GSM428063
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428063/suppl/GSM428063.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428064 | GPL570 |
|
PBMCs_Control_13
|
peripheral blood mononuclear cells
|
affected status: control
gender: male
age at examination: 26
geographical origin: Guarda
immunosuppressors: no
|
scan date 2
|
| Sample_geo_accession | GSM428064
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428064/suppl/GSM428064.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
| | |
|
GSM428065 | GPL570 |
|
PBMCs_Control_14
|
peripheral blood mononuclear cells
|
affected status: control
gender: male
age at examination: 21
geographical origin: Lisbon
immunosuppressors: no
|
scan date 2
|
| Sample_geo_accession | GSM428065
| | Sample_status | Public on Jul 01 2011
| | Sample_submission_date | Jul 15 2009
| | Sample_last_update_date | Jul 01 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Whole blood samples were obtained by venipuncture and collected in BD Vacutainer CPT tubes (BD, USA). PBMCs were isolated and their RNA stabilized using RNAlater (Qiagen, Germany) within three hours after sample collection.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was then extracted using the RNeasy Mini kit (Qiagen, Germany) according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA of each sample were prepared according to the standard Affymetrix protocol from 3.5 ug total RNA (Expression Analysis Technical Manual, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hours at 45 ºC on Affymetrix GeneChip Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip scanner 3000 – 7G.
| | Sample_data_processing | Affymetrix CEL files were analyzed together with their respective CDF (chip description file) file (HG-U133_Plus_2.cdf) on the Partek software (Partek Incorporated, USA). The background correction, normalization and summarization of the CEL files were deriveed using the robust multi-chip average (RMA) algorithm (with default settings of the Partek software: only perfect match values, derives quantile normalization across all the chips, and applies a log2 transformation to the intensities). Partek software was used to derive the adjusted data (ie.the expression value after correction for scan date, geographical origin, and immunosuppression status) in CORRECTED column.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Sofia,A,Oliveira
| | Sample_contact_email | soliveira@igc.gulbenkian.pt
| | Sample_contact_phone | +351 217 999 411
| | Sample_contact_fax | +351 217 999 412
| | Sample_contact_laboratory | P1C-76
| | Sample_contact_department | Edificio Egas Moniz
| | Sample_contact_institute | Instituto de Medicina Molecular
| | Sample_contact_address | Av. Prof Egas Moniz
| | Sample_contact_city | Lisbon
| | Sample_contact_state | Portugal
| | Sample_contact_zip/postal_code | 1649-028
| | Sample_contact_country | Portugal
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM428nnn/GSM428065/suppl/GSM428065.CEL.gz
| | Sample_series_id | GSE17114
| | Sample_data_row_count | 54675
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