Search results for the GEO ID: GSE23604 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM578886 | GPL570 |
|
patient Pre ECP, biological rep1
|
CTCL patient Pre ECP
|
disease state: cutaneous T cell lymphoma
dose: pre ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578886
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578886/suppl/GSM578886_KHOF_133-2_D13-0_030707.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578887 | GPL570 |
|
patient Pre ECP, biological rep2
|
CTCL patient Pre ECP
|
disease state: cutaneous T cell lymphoma
dose: pre ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578887
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578887/suppl/GSM578887_KHOF_133-2_D7-0_122006.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578888 | GPL570 |
|
patient Pre ECP, biological rep3
|
CTCL patient Pre ECP
|
disease state: cutaneous T cell lymphoma
dose: pre ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578888
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578888/suppl/GSM578888_KHOF_133-2_EMP2_122006.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578889 | GPL570 |
|
patient Pre ECP, biological rep4
|
GVHD patient Pre ECP
|
disease state: graft-versus host disease
dose: pre ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578889
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578889/suppl/GSM578889_KHOF_133-2_D17-0_031307.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578890 | GPL570 |
|
patient Pre ECP, biological rep5
|
GVHD patient Pre ECP
|
disease state: graft-versus host disease
dose: pre ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578890
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578890/suppl/GSM578890_KHOF_133-2_D19-0_030707.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578891 | GPL570 |
|
patient Pre ECP, biological rep6
|
GVHD patient Pre ECP
|
disease state: graft-versus host disease
dose: pre ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578891
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578891/suppl/GSM578891_KHOF_133-2_D10-0_122006.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578892 | GPL570 |
|
patient Post ECP, biological rep1
|
CTCL patient Post ECP
|
disease state: cutaneous T cell lymphoma
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578892
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578892/suppl/GSM578892_KHOF_133-2_EM10-18-P8_111706.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578893 | GPL570 |
|
patient Post ECP, biological rep2
|
CTCL patient Post ECP
|
disease state: cutaneous T cell lymphoma
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578893
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578893/suppl/GSM578893_KHOF_133-2_F13-1_030707.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578894 | GPL570 |
|
patient Post ECP, biological rep3
|
CTCL patient Post ECP
|
disease state: cutaneous T cell lymphoma
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578894
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578894/suppl/GSM578894_KHOF_133-2_F7-1_111706.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578895 | GPL570 |
|
patient Post ECP, biological rep4
|
GVHD patient Post ECP
|
disease state: graft-versus host disease
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578895
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578895/suppl/GSM578895_KHOF_133-2_F10-1_111706.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578896 | GPL570 |
|
patient Post ECP, biological rep5
|
GVHD patient Post ECP
|
disease state: graft-versus host disease
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578896
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578896/suppl/GSM578896_KHOF_133-2_F17-1_030707.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578897 | GPL570 |
|
patient Post ECP, biological rep6
|
GVHD patient Post ECP
|
disease state: graft-versus host disease
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578897
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578897/suppl/GSM578897_KHOF_133-2_F19-1_030707.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578898 | GPL570 |
|
normal Pre ECP, biological rep1
|
normal Pre ECP
|
disease state: normal
dose: pre ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578898
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578898/suppl/GSM578898_KHOF_133-2_42-0-LUCK_022908.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578899 | GPL570 |
|
normal Pre ECP, biological rep5
|
normal Pre ECP
|
disease state: normal
dose: pre ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578899
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578899/suppl/GSM578899_KHOF_133-2_B38-0_020108.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578900 | GPL570 |
|
normal Post ECP, biological rep1
|
normal Post ECP
|
disease state: normal
dose: post ECP
peripheral blood: Leukapheresis
|
Gene expression data
|
Sample_geo_accession | GSM578900
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578900/suppl/GSM578900_KHOF_133-2_2F38-1_020108.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578901 | GPL570 |
|
normal Pre ECP, biological rep2
|
normal Pre ECP
|
disease state: normal
dose: pre ECP
peripheral blood: blood harvested with the Therakos machine
|
Gene expression data
|
Sample_geo_accession | GSM578901
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578901/suppl/GSM578901_KHOF_133-2_47-1_032608.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578902 | GPL570 |
|
normal Pre ECP, biological rep3
|
normal Pre ECP
|
disease state: normal
dose: pre ECP
peripheral blood: blood harvested with the Therakos machine
|
Gene expression data
|
Sample_geo_accession | GSM578902
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578902/suppl/GSM578902_KHOF_133-2_48-1_052308.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578903 | GPL570 |
|
normal Pre ECP, biological rep4
|
normal Pre ECP
|
disease state: normal
dose: pre ECP
peripheral blood: blood harvested with the Therakos machine
|
Gene expression data
|
Sample_geo_accession | GSM578903
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578903/suppl/GSM578903_CBER_133-2_50-1_082708.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578904 | GPL570 |
|
normal Post ECP, biological rep2
|
normal Post ECP
|
disease state: normal
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578904
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578904/suppl/GSM578904_KHOF_133-2_42-1-BAG-ON_022908.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578905 | GPL570 |
|
normal Post ECP, biological rep3
|
normal Post ECP
|
disease state: normal
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578905
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578905/suppl/GSM578905_KHOF_133-2_47-4_032608.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578906 | GPL570 |
|
normal Post ECP, biological rep4
|
normal Post ECP
|
disease state: normal
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
this sample involved data from two arrays
|
Sample_geo_accession | GSM578906
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578906/suppl/GSM578906_KHOF_133-2_48-5_052308.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578906/suppl/GSM578906_KHOF_133-2_48-6_052308.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578906 | GPL570 |
|
normal Post ECP, biological rep4
|
normal Post ECP
|
disease state: normal
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
this sample involved data from two arrays
|
Sample_geo_accession | GSM578906
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578906/suppl/GSM578906_KHOF_133-2_48-5_052308.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578906/suppl/GSM578906_KHOF_133-2_48-6_052308.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578907 | GPL570 |
|
normal Post ECP, biological rep5
|
normal Post ECP
|
disease state: normal
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
Gene expression data
|
Sample_geo_accession | GSM578907
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578907/suppl/GSM578907_CBER_133-2_49-5-2_070908.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578908 | GPL570 |
|
normal Post ECP, biological rep6
|
normal Post ECP
|
disease state: normal
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
this sample involved data from two arrays
|
Sample_geo_accession | GSM578908
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578908/suppl/GSM578908_CBER_133-2_50-5_082708.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578908/suppl/GSM578908_CBER_133-2_50-6_082708.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
GSM578908 | GPL570 |
|
normal Post ECP, biological rep6
|
normal Post ECP
|
disease state: normal
dose: post ECP
peripheral blood: Treated with ECP and Incubated overnight
|
this sample involved data from two arrays
|
Sample_geo_accession | GSM578908
| Sample_status | Public on Aug 14 2010
| Sample_submission_date | Aug 12 2010
| Sample_last_update_date | Aug 13 2010
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Samples were obtained from the Therakos machine Pre Tx, and Post ECP after overnight incubation in a platelet storage bag with RPMI 1640 and 15% serum
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy Mini Kit columns with on-column Dnase I treatment (Qiagen).
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1ug or 10ng of total RNA was amplified using the affymetrix one cycle or two cycle amplification(in conjunction with the T7megscript kit[Ambion]) kits respectively following the manufacturers protocols
| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on GeneChip HG U133+2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| Sample_scan_protocol | GCOS 1.2
| Sample_data_processing | Raw data without normalization generated from Affymetrix Gene Chip Operating Software Version 1.2 were analyzed using GeneSpring software 7.2. Data was normalized using Robust Multi-Array. Probe sets with a minimal fold change of >2.0 combined with an average signal intensity of 500 or higher were included in the analysis. Differential gene expression was considered as a >2 fold change and a p value of <0.05. The data was corrected using the false discovery rate (FDR) technique to adjust he p-values.
| Sample_platform_id | GPL570
| Sample_contact_name | Carole,L.,Berger
| Sample_contact_email | carole.berger@yale.edu
| Sample_contact_phone | 203 737-4024
| Sample_contact_fax | 203-785-7637
| Sample_contact_laboratory | LCI 509
| Sample_contact_department | Dermatology
| Sample_contact_institute | Yale University
| Sample_contact_address | 333 Cedar Street
| Sample_contact_city | New Haven
| Sample_contact_state | CT
| Sample_contact_zip/postal_code | 06520
| Sample_contact_country | USA
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578908/suppl/GSM578908_CBER_133-2_50-5_082708.CEL.gz
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM578nnn/GSM578908/suppl/GSM578908_CBER_133-2_50-6_082708.CEL.gz
| Sample_series_id | GSE23604
| Sample_data_row_count | 54675
| |
|
|
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Make groups for comparisons |
(2 groups will be compared at a time) |
|
Select GSMs and click on "Add groups" |
Enter the group name here: |
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