Search results for the GEO ID: GSE16461  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM413790 | GPL570 |
|
Healthy CD4+T cells 1-TP
|
CD4+T cells
|
disease state: Healthy
cell type: CD4+T
twin: T
|
n/a
|
| Sample_geo_accession | GSM413790
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413790/suppl/GSM413790.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413791 | GPL570 |
|
Multiple sclerosis CD4+T cells 3-TE
|
CD4+T cells
|
disease state: Multiple sclerosis
cell type: CD4+T
twin: T
|
n/a
|
| Sample_geo_accession | GSM413791
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413791/suppl/GSM413791.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413792 | GPL570 |
|
Healthy CD4+T cells 5-PS
|
CD4+T cells
|
disease state: Healthy
cell type: CD4+T
twin: P
|
n/a
|
| Sample_geo_accession | GSM413792
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413792/suppl/GSM413792.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413793 | GPL570 |
|
Multiple sclerosis CD4+T cells 7-PM
|
CD4+T cells
|
disease state: Multiple sclerosis
cell type: CD4+T
twin: P
|
n/a
|
| Sample_geo_accession | GSM413793
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413793/suppl/GSM413793.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413794 | GPL570 |
|
Multiple sclerosis CD4+T cells 9-RS
|
CD4+T cells
|
disease state: Multiple sclerosis
cell type: CD4+T
twin: R
|
n/a
|
| Sample_geo_accession | GSM413794
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413794/suppl/GSM413794.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413795 | GPL570 |
|
Healthy CD4+T cells 11-RP
|
CD4+T cells
|
disease state: Healthy
cell type: CD4+T
twin: R
|
n/a
|
| Sample_geo_accession | GSM413795
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413795/suppl/GSM413795.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413796 | GPL570 |
|
Healthy CD4+T cells 13-UD
|
CD4+T cells
|
disease state: Healthy
cell type: CD4+T
twin: U
|
n/a
|
| Sample_geo_accession | GSM413796
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413796/suppl/GSM413796.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413797 | GPL570 |
|
Multiple sclerosis CD4+T cells 15-US
|
CD4+T cells
|
disease state: Multiple sclerosis
cell type: CD4+T
twin: U
|
n/a
|
| Sample_geo_accession | GSM413797
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413797/suppl/GSM413797.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413798 | GPL570 |
|
Healthy CD8+T cells 2-TP
|
CD8+T cells
|
disease state: Healthy
cell type: CD8+T
twin: T
|
n/a
|
| Sample_geo_accession | GSM413798
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413798/suppl/GSM413798.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413799 | GPL570 |
|
Multiple sclerosis CD8+T cells 4-TE
|
CD8+T cells
|
disease state: Multiple sclerosis
cell type: CD8+T
twin: T
|
n/a
|
| Sample_geo_accession | GSM413799
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413799/suppl/GSM413799.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413800 | GPL570 |
|
Healthy CD8+T cells 6-PS
|
CD8+T cells
|
disease state: Healthy
cell type: CD8+T
twin: P
|
n/a
|
| Sample_geo_accession | GSM413800
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413800/suppl/GSM413800.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413801 | GPL570 |
|
Multiple sclerosis CD8+T cells 8-PM
|
CD8+T cells
|
disease state: Multiple sclerosis
cell type: CD8+T
twin: P
|
n/a
|
| Sample_geo_accession | GSM413801
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413801/suppl/GSM413801.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413802 | GPL570 |
|
Multiple sclerosis CD8+T cells 10-RS
|
CD8+T cells
|
disease state: Multiple sclerosis
cell type: CD8+T
twin: R
|
n/a
|
| Sample_geo_accession | GSM413802
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413802/suppl/GSM413802.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413803 | GPL570 |
|
Healthy CD8+T cells 12-RP
|
CD8+T cells
|
disease state: Healthy
cell type: CD8+T
twin: R
|
n/a
|
| Sample_geo_accession | GSM413803
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413803/suppl/GSM413803.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413804 | GPL570 |
|
Healthy CD8+T cells 14-UD
|
CD8+T cells
|
disease state: Healthy
cell type: CD8+T
twin: U
|
n/a
|
| Sample_geo_accession | GSM413804
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413804/suppl/GSM413804.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
GSM413805 | GPL570 |
|
Multiple sclerosis CD8+T cells 16-US
|
CD8+T cells
|
disease state: Multiple sclerosis
cell type: CD8+T
twin: U
|
n/a
|
| Sample_geo_accession | GSM413805
| | Sample_status | Public on Dec 31 2010
| | Sample_submission_date | Jun 05 2009
| | Sample_last_update_date | Dec 31 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For gene expression profiling, peripheral blood mononuclear cell (PBMC) were obtained from leukopheresis by density centrifugation over Ficoll-hypaque according to standard procedures. Briefly, heparinized blood was diluted with 1 volume of RPMI medium and gently layered over the Fycoll. Following centrifugation at 660 g for 30 minutes, cells at the interface of the gradient was collected and washed 3 times. Highly purified CD4+ and CD8+ (purity >95%) cell subsets were then sorted by flow cytometry on MoFlo high speed cell sorter (Beckman Coulter, Fullerton, CA) and frozen in Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | none
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix® GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The statistical analysis was performed couple by couple using the Rosetta Resolver® system (Rosetta Biosoftware). The fold-change of each gene was calculated by comparing gene expression in the affected twin with that in the unaffected twin and the genes with the same trend in at least 3 twin pairs out of the 4 studied were selected as candidates to be validated by real-time RT-PCR.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Viviana,,Annibali
| | Sample_contact_email | viviana.annibali@uniroma1.it
| | Sample_contact_phone | +390633775562
| | Sample_contact_fax | +390633775900
| | Sample_contact_laboratory | DiMA S3
| | Sample_contact_institute | University of Rome "Sapienza"
| | Sample_contact_address | Via di Grottarossa,1035
| | Sample_contact_city | Rome
| | Sample_contact_zip/postal_code | 00189
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM413nnn/GSM413805/suppl/GSM413805.CEL.gz
| | Sample_series_id | GSE16461
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
Enter the group name here: |
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