Search results for the GEO ID: GSE17269  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM432521 | GPL570 |
|
HD naive B cell, biological rep1
|
Peripheral blood ex vivo naive B cells of HD
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38+CD21+
diagnosis: healthy donor
cell type: naive B cell
|
Gene expression data from ex vivo naive B cells of HD
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432521
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432521/suppl/GSM432521_HD-naive-1.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432522 | GPL570 |
|
HD naive B cell, biological rep2
|
Peripheral blood ex vivo naive B cells of HD
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38+CD21+
diagnosis: healthy donor
cell type: naive B cell
|
Gene expression data from ex vivo naive B cells of HD
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432522
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432522/suppl/GSM432522_HD-naive-2.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432523 | GPL570 |
|
HD naive B cell, biological rep3
|
Peripheral blood ex vivo naive B cells of HD
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38+CD21+
diagnosis: healthy donor
cell type: naive B cell
|
Gene expression data from ex vivo naive B cells of HD
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432523
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432523/suppl/GSM432523_HD-naive-3.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432524 | GPL570 |
|
HD naive B cell, biological rep4
|
Peripheral blood ex vivo naive B cells of HD
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38+CD21+
diagnosis: healthy donor
cell type: naive B cell
|
Gene expression data from ex vivo naive B cells of HD
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432524
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432524/suppl/GSM432524_HD-naive-4.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432525 | GPL570 |
|
CVID naive B cell, biological rep1
|
Peripheral blood ex vivo naive B cells of CVID patient
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38+CD21+
diagnosis: CVID
cell type: naive B cell
|
Gene expression data from ex vivo naive B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432525
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432525/suppl/GSM432525_CVID-naive-1.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432526 | GPL570 |
|
CVID naive B cell, biological rep2
|
Peripheral blood ex vivo naive B cells of CVID patient
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38+CD21+
diagnosis: CVID
cell type: naive B cell
|
Gene expression data from ex vivo naive B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432526
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432526/suppl/GSM432526_CVID-naive-2.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432527 | GPL570 |
|
CVID naive B cell, biological rep3
|
Peripheral blood ex vivo naive B cells of CVID patient
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38+CD21+
diagnosis: CVID
cell type: naive B cell
|
Gene expression data from ex vivo naive B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432527
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432527/suppl/GSM432527_CVID-naive-3.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432528 | GPL570 |
|
CVID CD21low B cell, biological rep1
|
Peripheral blood ex vivo CD21low B cells of CVID patient
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38lowCD21low
diagnosis: CVID
cell type: CD21low B cell
|
Gene expression data from ex vivo CD21low B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432528
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432528/suppl/GSM432528_CVID-CD21low-1.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432529 | GPL570 |
|
CVID CD21low B cell, biological rep2
|
Peripheral blood ex vivo CD21low B cells of CVID patient
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38lowCD21low
diagnosis: CVID
cell type: CD21low B cell
|
Gene expression data from ex vivo CD21low B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432529
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432529/suppl/GSM432529_CVID-CD21low-2.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432530 | GPL570 |
|
CVID CD21low B cell, biological rep3
|
Peripheral blood ex vivo CD21low B cells of CVID patient
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38lowCD21low
diagnosis: CVID
cell type: CD21low B cell
|
Gene expression data from ex vivo CD21low B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432530
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432530/suppl/GSM432530_CVID-CD21low-3.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
|
GSM432531 | GPL570 |
|
CVID CD21low B cell, biological rep4
|
Peripheral blood ex vivo CD21low B cells of CVID patient
|
protocol: sorted ex vivo cells
phenotype: CD19+CD27-CD38lowCD21low
diagnosis: CVID
cell type: CD21low B cell
|
Gene expression data from ex vivo CD21low B cells of CVID
Ficoll gradient separated periphreal blood mononuclear cells were stained for the expression of CD19, CD21, CD27 and CD38 cell surface markers. The cells were sorted into CD19+CD27-CD38+CD21+ naive B cells and CD19hiCD27-CD38lowCD21low B cells.
|
| Sample_geo_accession | GSM432531
| | Sample_status | Public on Jul 30 2009
| | Sample_submission_date | Jul 23 2009
| | Sample_last_update_date | Jul 30 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | No treatment, ex vivo cells
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using GeneChip® Two-Cycle Target Labeling kit according to the Affymetrix protocol from 100 ng total RNA (GeneChip® Expression Analysis Technical Manual, 2005-2006, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 Plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip® Scanner 3000.
| | Sample_data_processing | Microarray Suite version 5.0 (MAS 5.0) software was used to generate CEL files using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500. The CEL files were uploaded and analyzed using the dCHIP software. The signal intensities were logged, normalized using invariant set normalization method and model-based expression values were calculated.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Mirzokhid,,Rakhmanov
| | Sample_contact_email | mirzokhid.rakhmanov@uniklinik-freiburg.de
| | Sample_contact_phone | +49 761 270 6314
| | Sample_contact_fax | +49 761 270 6378
| | Sample_contact_laboratory | AG Warnatz
| | Sample_contact_department | Centre of Chronic Immunodeficiency
| | Sample_contact_institute | University Medical Center Freiburg
| | Sample_contact_address | Breisacher Str. 66
| | Sample_contact_city | Freiburg i. Breisgau
| | Sample_contact_state | BW
| | Sample_contact_zip/postal_code | D-79106
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM432nnn/GSM432531/suppl/GSM432531_CVID-CD21low-4.CEL.gz
| | Sample_series_id | GSE17269
| | Sample_data_row_count | 54613
| | |
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