Search results for the GEO ID: GSE24147  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM594299 | GPL570 |
|
U-937 cells, recent-onset type I diabetes sera, rep1
|
U-937 cells stimulated with recent-onset type I diabetes sera
|
cell line: U-937
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_RO1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594299
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594299/suppl/GSM594299.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594300 | GPL570 |
|
U-937 cells, recent-onset type I diabetes sera, rep2
|
U-937 cells stimulated with recent-onset type I diabetes sera
|
cell line: U-937
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_RO2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594300
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594300/suppl/GSM594300.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594301 | GPL570 |
|
U-937 cells, recent-onset type I diabetes sera, rep3
|
U-937 cells stimulated with recent-onset type I diabetes sera
|
cell line: U-937
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_RO3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594301
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594301/suppl/GSM594301.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594302 | GPL570 |
|
U-937 cells, healthy control sera, rep1
|
U-937 cells stimulated with healthy-control sera
|
cell line: U-937
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_HC1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594302
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594302/suppl/GSM594302.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594303 | GPL570 |
|
U-937 cells, healthy control sera, rep2
|
U-937 cells stimulated with healthy-control sera
|
cell line: U-937
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_HC2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594303
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594303/suppl/GSM594303.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594304 | GPL570 |
|
U-937 cells, healthy control sera, rep3
|
U-937 cells stimulated with healthy-control sera
|
cell line: U-937
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
U-937_HC3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594304
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594304/suppl/GSM594304.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594305 | GPL570 |
|
THP-1 cells, recent-onset type I diabetes sera, rep1
|
THP-1 cells stimulated with recent-onset type I diabetes sera
|
cell line: THP-1
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_RO1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594305
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594305/suppl/GSM594305.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594306 | GPL570 |
|
THP-1 cells, recent-onset type I diabetes sera, rep2
|
THP-1 cells stimulated with recent-onset type I diabetes sera
|
cell line: THP-1
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_RO2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594306
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594306/suppl/GSM594306.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594307 | GPL570 |
|
THP-1 cells, recent-onset type I diabetes sera, rep3
|
THP-1 cells stimulated with recent-onset type I diabetes sera
|
cell line: THP-1
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_RO3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594307
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594307/suppl/GSM594307.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594308 | GPL570 |
|
THP-1 cells, healthy control sera, rep1
|
THP-1 cells stimulated with healthy-control sera
|
cell line: THP-1
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_HC1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594308
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594308/suppl/GSM594308.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594309 | GPL570 |
|
THP-1 cells, healthy control sera, rep2
|
THP-1 cells stimulated with healthy-control sera
|
cell line: THP-1
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_HC2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594309
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594309/suppl/GSM594309.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594310 | GPL570 |
|
THP-1 cells, healthy control sera, rep3
|
THP-1 cells stimulated with healthy-control sera
|
cell line: THP-1
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
THP-1_HC3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594310
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594310/suppl/GSM594310.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594311 | GPL570 |
|
KG-1 cells, recent-onset type I diabetes sera, rep1
|
KG1 cells stimulated with recent-onset type I diabetes sera
|
cell line: KG1
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_RO1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594311
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594311/suppl/GSM594311.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594312 | GPL570 |
|
KG-1 cells, recent-onset type I diabetes sera, rep2
|
KG1 cells stimulated with recent-onset type I diabetes sera
|
cell line: KG1
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_RO2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594312
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594312/suppl/GSM594312.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594313 | GPL570 |
|
KG-1 cells, recent-onset type I diabetes sera, rep3
|
KG1 cells stimulated with recent-onset type I diabetes sera
|
cell line: KG1
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_RO3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594313
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594313/suppl/GSM594313.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594314 | GPL570 |
|
KG-1 cells, healthy control sera, rep1
|
KG1 cells stimulated with healthy-control sera
|
cell line: KG1
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_HC1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594314
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594314/suppl/GSM594314.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594315 | GPL570 |
|
KG-1 cells, healthy control sera, rep2
|
KG1 cells stimulated with healthy-control sera
|
cell line: KG1
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_HC2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594315
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594315/suppl/GSM594315.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594316 | GPL570 |
|
KG-1 cells, healthy control sera, rep3
|
KG1 cells stimulated with healthy-control sera
|
cell line: KG1
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
KG-1_HC3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594316
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594316/suppl/GSM594316.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594317 | GPL570 |
|
K562 cells, recent-onset type I diabetes sera, rep1
|
K562 cells stimulated with recent-onset type I diabetes sera
|
cell line: K562
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
K562_RO1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594317
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594317/suppl/GSM594317.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594318 | GPL570 |
|
K562 cells, recent-onset type I diabetes sera, rep2
|
K562 cells stimulated with recent-onset type I diabetes sera
|
cell line: K562
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
K562_RO2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594318
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594318/suppl/GSM594318.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594319 | GPL570 |
|
K562 cells, recent-onset type I diabetes sera, rep3
|
K562 cells stimulated with recent-onset type I diabetes sera
|
cell line: K562
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
K562_RO3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594319
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594319/suppl/GSM594319.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594320 | GPL570 |
|
K562 cells, healthy control sera, rep1
|
K562 cells stimulated with healthy-control sera
|
cell line: K562
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
K562_HC1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594320
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594320/suppl/GSM594320.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594321 | GPL570 |
|
K562 cells, healthy control sera, rep2
|
K562 cells stimulated with healthy-control sera
|
cell line: K562
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
K562_HC2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594321
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594321/suppl/GSM594321.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594322 | GPL570 |
|
K562 cells, healthy control sera, rep3
|
K562 cells stimulated with healthy-control sera
|
cell line: K562
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
K562_HC3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594322
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594322/suppl/GSM594322.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594323 | GPL570 |
|
IM9 cells, recent-onset type I diabetes sera, rep1
|
IM9 cells stimulated with recent-onset type I diabetes sera
|
cell line: IM9
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_RO1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594323
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594323/suppl/GSM594323.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594324 | GPL570 |
|
IM9 cells, recent-onset type I diabetes sera, rep2
|
IM9 cells stimulated with recent-onset type I diabetes sera
|
cell line: IM9
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_RO2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594324
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594324/suppl/GSM594324.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594325 | GPL570 |
|
IM9 cells, recent-onset type I diabetes sera, rep3
|
IM9 cells stimulated with recent-onset type I diabetes sera
|
cell line: IM9
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_RO3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594325
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594325/suppl/GSM594325.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594326 | GPL570 |
|
IM9 cells, healthy control sera, rep1
|
IM9 cells stimulated with healthy-control sera
|
cell line: IM9
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_HC1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594326
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594326/suppl/GSM594326.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594327 | GPL570 |
|
IM9 cells, healthy control sera, rep2
|
IM9 cells stimulated with healthy-control sera
|
cell line: IM9
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_HC2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594327
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594327/suppl/GSM594327.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594328 | GPL570 |
|
IM9 cells, healthy control sera, rep3
|
IM9 cells stimulated with healthy-control sera
|
cell line: IM9
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
IM9_HC3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594328
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594328/suppl/GSM594328.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594329 | GPL570 |
|
HL-60 cells, recent-onset type I diabetes sera, rep1
|
HL-60 cells stimulated with recent-onset type I diabetes sera
|
cell line: HL-60
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_RO1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594329
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594329/suppl/GSM594329.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594330 | GPL570 |
|
HL-60 cells, recent-onset type I diabetes sera, rep2
|
HL-60 cells stimulated with recent-onset type I diabetes sera
|
cell line: HL-60
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_RO2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594330
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594330/suppl/GSM594330.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594331 | GPL570 |
|
HL-60 cells, recent-onset type I diabetes sera, rep3
|
HL-60 cells stimulated with recent-onset type I diabetes sera
|
cell line: HL-60
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_RO3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594331
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594331/suppl/GSM594331.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594332 | GPL570 |
|
HL-60 cells, healthy control sera, rep1
|
HL-60 cells stimulated with healthy-control sera
|
cell line: HL-60
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_HC1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594332
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594332/suppl/GSM594332.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594333 | GPL570 |
|
HL-60 cells, healthy control sera, rep2
|
HL-60 cells stimulated with healthy-control sera
|
cell line: HL-60
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_HC2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594333
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594333/suppl/GSM594333.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594334 | GPL570 |
|
HL-60 cells, healthy control sera, rep3
|
HL-60 cells stimulated with healthy-control sera
|
cell line: HL-60
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
HL-60_HC3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594334
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594334/suppl/GSM594334.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594335 | GPL570 |
|
CCRF-CEM cells, recent-onset type I diabetes sera, rep1
|
CCRF-CEM cells stimulated with recent-onset type I diabetes sera
|
cell line: CCRF-CEM
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_RO1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594335
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594335/suppl/GSM594335.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594336 | GPL570 |
|
CCRF-CEM cells, recent-onset type I diabetes sera, rep2
|
CCRF-CEM cells stimulated with recent-onset type I diabetes sera
|
cell line: CCRF-CEM
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_RO2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594336
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594336/suppl/GSM594336.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594337 | GPL570 |
|
CCRF-CEM cells, recent-onset type I diabetes sera, rep3
|
CCRF-CEM cells stimulated with recent-onset type I diabetes sera
|
cell line: CCRF-CEM
treatment: recent-onset type I diabetes sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_RO3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594337
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594337/suppl/GSM594337.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594338 | GPL570 |
|
CCRF-CEM cells, healthy control sera, rep1
|
CCRF-CEM cells stimulated with healthy-control sera
|
cell line: CCRF-CEM
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_HC1
Biological replicate 1 of 3.
|
| Sample_geo_accession | GSM594338
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594338/suppl/GSM594338.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594339 | GPL570 |
|
CCRF-CEM cells, healthy control sera, rep2
|
CCRF-CEM cells stimulated with healthy-control sera
|
cell line: CCRF-CEM
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_HC2
Biological replicate 2 of 3.
|
| Sample_geo_accession | GSM594339
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594339/suppl/GSM594339.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
GSM594340 | GPL570 |
|
CCRF-CEM cells, healthy control sera, rep3
|
CCRF-CEM cells stimulated with healthy-control sera
|
cell line: CCRF-CEM
treatment: health control sera
|
Gene expression data from cell lines stimulated with RO or HC sera.
CCRF-CEM_HC3
Biological replicate 3 of 3.
|
| Sample_geo_accession | GSM594340
| | Sample_status | Public on Sep 16 2010
| | Sample_submission_date | Sep 15 2010
| | Sample_last_update_date | Sep 15 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Seven myeloid/lymphoid cell lines (K562: chronic myelogenous leukemia; IM9: B-lymphoblastic; HL-60: acute myeloid leukemia; KG-1: erythroleukemia; CCRF-CEM: T-acute lymphoblastic leukemia; THP-1: acute monocytic leukemia; U-937: myelomonocytic lymphoma) were purchased from the American Tissue Culture Collection (ATCC, Manassas, VA, USA). These were selected on the basis of their original cell type, properties and characteristics. Cells were grown in complete media per the provider’s product information sheets with 100U/ml Penicillin and 100ug/ml Streptomycin. The induction of gene expression was accomplished by culturing each of the seven cell lines for 6 h at 37°C in 5% CO2 with pooled healthy control sera or pooled recent-onset T1D sera (n=20 individual sera). Cultures were prepared in a Costar 24-well plate (Corning, Corning NY) using 3 wells per condition (500,000 cells/well in 400 µl of RPMI 1640 medium plus 100 µl (20%) of plasma. After culture, the content of each well was centrifuged, and the pellet lysed/resuspended by vortexing in 1ml of Trizol (Invitrogen).
| | Sample_growth_protocol_ch1 | Recent-onset T1D patients (after stabilization on exogenous insulin but within 7 months post-onset; n=20, all Caucasian) were recruited through Children’s Hospital of Wisconsin. Diabetes was defined according to World Health Organization criteria and included blood glucose levels of >200 mg/dl with symptoms confirmed by a physician. Healthy Caucasian control (n=20) criteria included fasting blood glucose of <100 mg/dl, no familial history of any autoimmune disorder, and negativity for islet auto-antibodies at the 99th percentile. All study subjects were free of known infection at the time of sample collection. All peripheral blood samples were drawn by trained phlebotomists at Children’s Hospital of Wisconsin. Peripheral blood was aseptically collected in acid citrate dextrose solution A or K+EDTA anti-coagulant and components were immediately separated by Ficoll-Histopaque density gradient centrifugation. sera was stored at –80°C until use.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted and amplified using an Affymetrix two-cycle cDNA synthesis kit (Affymetrix, Santa Clara, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | cRNA was synthesized and labeled in accordance to the Affymetrix GeneChip expression analysis technical manual.
| | Sample_hyb_protocol | The GeneChip human genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage. cRNA was fragmented and hybridized to the array in accordance to the Affymetrix GeneChip expression analysis technical manual. After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001.
| | Sample_scan_protocol | Arrays were scanned with a 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | Image data were analyzed with Affymetrix GeneChip operating software (GCOS) and normalized with Robust Multichip Analysis (RMA) in Bioconductor (www.bioconductor.org/) to determine the log2 signals. Each of the triplicate cultures was independently analyzed (6 arrays per cell line, 42 arrays in total). The statistical significance of differential gene expression and false discovery rates (FDR) were derived through a Rank Product algorithm available as an analysis package in R.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Martin,,Hessner
| | Sample_contact_email | mhessner@mcw.edu
| | Sample_contact_phone | 414-456-4496
| | Sample_contact_fax | 414-456-6663
| | Sample_contact_laboratory | Max McGee National Research Center for Juvenile Diabetes
| | Sample_contact_department | Pediatrics
| | Sample_contact_institute | Medical College of Wisconsin
| | Sample_contact_address | 8701 Watertown Plank Road
| | Sample_contact_city | Milwaukee
| | Sample_contact_state | WI
| | Sample_contact_zip/postal_code | 53226
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.mcw.edu/MaxMcGeeResearchCenter.htm
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM594nnn/GSM594340/suppl/GSM594340.CEL.gz
| | Sample_series_id | GSE24147
| | Sample_data_row_count | 54675
| | |
|
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