Search results for the GEO ID: GSE42660  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1047538 | GPL570 |
|
ASBatch1_rhBAFF_Nr.6
|
BL2_rhBAFF_9hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhBAFF for 9hrs
biological replicate: 1
|
ASBatch1_BAFF.Nr.6
|
| Sample_geo_accession | GSM1047538
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047538/suppl/GSM1047538_ASBatch1_BAFF_Nr.6.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047539 | GPL570 |
|
ASBatch1_antiIgM F(ab) fragments_Nr.7
|
BL2_antiIgM F(ab) fragments_3hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: antiIgM F(ab) fragments for 3hrs
biological replicate: 1
|
ASBatch1_BCR.Nr.7
|
| Sample_geo_accession | GSM1047539
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047539/suppl/GSM1047539_ASBatch1_BCR_Nr.7.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047540 | GPL570 |
|
ASBatch1_rhCD40L_A_Nr.2
|
BL2_rhCD40L_30min
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhCD40L for 30min
biological replicate: 1
|
ASBatch1_CD40_A.Nr.2
|
| Sample_geo_accession | GSM1047540
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047540/suppl/GSM1047540_ASBatch1_CD40_A_Nr.2.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047541 | GPL570 |
|
ASBatch1_rhCD40L_B_Nr.3
|
BL2_rhCD40L_6hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhCD40L for 6hrs
biological replicate: 1
|
ASBatch1_CD40_B.Nr.3
|
| Sample_geo_accession | GSM1047541
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047541/suppl/GSM1047541_ASBatch1_CD40_B_Nr.3.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047542 | GPL570 |
|
ASBatch1_rhIL21_Nr.8
|
BL2_rhIL21_2hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhIL21 for 2hrs
biological replicate: 1
|
ASBatch1_IL21.Nr.8
|
| Sample_geo_accession | GSM1047542
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047542/suppl/GSM1047542_ASBatch1_IL21_Nr.8.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047543 | GPL570 |
|
ASBatch1_Kontrolle_Nr.1
|
BL2_none (control)
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: none (control)
biological replicate: 1
|
ASBatch1_Kontrolle.Nr.1
|
| Sample_geo_accession | GSM1047543
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047543/suppl/GSM1047543_ASBatch1_Kontrolle_Nr.1.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047544 | GPL570 |
|
ASBatch1_LPS_A_Nr.4
|
BL2_LPS_30mins
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: LPS for 30mins
biological replicate: 1
|
ASBatch1_LPS_A.Nr.4
|
| Sample_geo_accession | GSM1047544
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047544/suppl/GSM1047544_ASBatch1_LPS_A_Nr.4.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047545 | GPL570 |
|
ASBatch1_LPS_B_Nr.5
|
BL2_LPS_6hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: LPS for 6hrs
biological replicate: 1
|
ASBatch1_LPS_B.Nr.5
|
| Sample_geo_accession | GSM1047545
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047545/suppl/GSM1047545_ASBatch1_LPS_B_Nr.5.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047546 | GPL570 |
|
ASBatch2_rhBAFF_Nr.14
|
BL2_rhBAFF_9hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhBAFF for 9hrs
biological replicate: 2
|
ASBatch2_BAFF.Nr.14
|
| Sample_geo_accession | GSM1047546
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047546/suppl/GSM1047546_ASBatch2_BAFF_Nr.14.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047547 | GPL570 |
|
ASBatch2_antiIgM F(ab) fragments_Nr.15
|
BL2_antiIgM F(ab) fragments_3hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: antiIgM F(ab) fragments for 3hrs
biological replicate: 2
|
ASBatch2_BCR.Nr.15
|
| Sample_geo_accession | GSM1047547
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047547/suppl/GSM1047547_ASBatch2_BCR_Nr.15.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047548 | GPL570 |
|
ASBatch2_rhCD40L_A_Nr.10
|
BL2_rhCD40L_30min
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhCD40L for 30min
biological replicate: 2
|
ASBatch2_CD40_A.Nr.10
|
| Sample_geo_accession | GSM1047548
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047548/suppl/GSM1047548_ASBatch2_CD40_A_Nr.10.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047549 | GPL570 |
|
ASBatch2_rhCD40L_B_Nr.11
|
BL2_rhCD40L_6hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhCD40L for 6hrs
biological replicate: 2
|
ASBatch2_CD40_B.Nr.11
|
| Sample_geo_accession | GSM1047549
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047549/suppl/GSM1047549_ASBatch2_CD40_B_Nr.11.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047550 | GPL570 |
|
ASBatch2_rhIL21_Nr.16
|
BL2_rhIL21_2hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhIL21 for 2hrs
biological replicate: 2
|
ASBatch2_IL21.Nr.16
|
| Sample_geo_accession | GSM1047550
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047550/suppl/GSM1047550_ASBatch2_IL21_Nr.16.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047551 | GPL570 |
|
ASBatch2_Kontrolle_Nr.9
|
BL2_none (control)
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: none (control)
biological replicate: 2
|
ASBatch2_Kontrolle.Nr.9
|
| Sample_geo_accession | GSM1047551
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047551/suppl/GSM1047551_ASBatch2_Kontrolle_Nr.9.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047552 | GPL570 |
|
ASBatch2_LPS_A_Nr.12
|
BL2_LPS_30mins
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: LPS for 30mins
biological replicate: 2
|
ASBatch2_LPS_A.Nr.12
|
| Sample_geo_accession | GSM1047552
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047552/suppl/GSM1047552_ASBatch2_LPS_A_Nr.12.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047553 | GPL570 |
|
ASBatch2_LPS_B_Nr.13
|
BL2_LPS_6hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: LPS for 6hrs
biological replicate: 2
|
ASBatch2_LPS_B.Nr.13
|
| Sample_geo_accession | GSM1047553
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047553/suppl/GSM1047553_ASBatch2_LPS_B_Nr.13.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047554 | GPL570 |
|
ASBatch3_rhBAFF_B_Nr.20
|
BL2_rhBAFF_9hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhBAFF for 9hrs
biological replicate: 3
|
ASBatch3_BAFF_B.Nr.20
|
| Sample_geo_accession | GSM1047554
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047554/suppl/GSM1047554_ASBatch3_BAFF_B_Nr.20.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047555 | GPL570 |
|
ASBatch3_antiIgM F(ab) fragments_Nr.21
|
BL2_antiIgM F(ab) fragments_3hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: antiIgM F(ab) fragments for 3hrs
biological replicate: 3
|
ASBatch3_BCR.Nr.21
|
| Sample_geo_accession | GSM1047555
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047555/suppl/GSM1047555_ASBatch3_BCR_Nr.21.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047556 | GPL570 |
|
ASBatch3_rhCD40L_B_Nr.18
|
BL2_rhCD40L_6hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhCD40L for 6hrs
biological replicate: 3
|
ASBatch3_CD40_B.Nr.18
|
| Sample_geo_accession | GSM1047556
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047556/suppl/GSM1047556_ASBatch3_CD40_B_Nr.18.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047557 | GPL570 |
|
ASBatch3_rhIL21_Nr.22
|
BL2_rhIL21_2hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: rhIL21 for 2hrs
biological replicate: 3
|
ASBatch3_IL21.Nr.22
|
| Sample_geo_accession | GSM1047557
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047557/suppl/GSM1047557_ASBatch3_IL21_Nr.22.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047558 | GPL570 |
|
ASBatch3_Kontrolle_Nr.17
|
BL2_none (control)
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: none (control)
biological replicate: 3
|
ASBatch3_Kontrolle.Nr.17
|
| Sample_geo_accession | GSM1047558
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047558/suppl/GSM1047558_ASBatch3_Kontrolle_Nr.17.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
| | |
|
GSM1047559 | GPL570 |
|
ASBatch3_LPS_B_Nr.19
|
BL2_LPS_6hrs
|
cell line: BL2
cell type: Burkitt Lymphoma cells
treated with: LPS for 6hrs
biological replicate: 3
|
ASBatch3_LPS_B.Nr.19
|
| Sample_geo_accession | GSM1047559
| | Sample_status | Public on Feb 01 2013
| | Sample_submission_date | Nov 30 2012
| | Sample_last_update_date | Feb 02 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | treatment of BL2 cells with recombinant proteins/antibodies for indicated timepoints
| | Sample_growth_protocol_ch1 | BL2 cells in RPMI containing 10% FCS
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen RNA-isolation
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared from 0,3 µg totalRNA according to the Affymetrix GeneChip 3’ IVT Express Kit manual (Rev. 6)
| | Sample_hyb_protocol | Following fragmentation, 12.5 μg of cRNA were hybridized for 16 h at 45°C on GeneChip Human Genome U133 Plus 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Gene expression values were obtained by first removing the background and normalizing on probe level using the variance stabilization method by Huber and colleagues. The normalized probe intensities were summarized into gene expression levels by using an additive model fitted by the median polish procedure. The publically available software packages cited here are used to implement this module. The BioConductor packages affy and vsn were used for reading, normalization and summarization.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Katharina,,Meyer
| | Sample_contact_department | Statistical Bioinformatics
| | Sample_contact_institute | Institute for Functional Genomics
| | Sample_contact_address | Josef Engert Street 9
| | Sample_contact_city | Regensburg
| | Sample_contact_zip/postal_code | 93049
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1047nnn/GSM1047559/suppl/GSM1047559_ASBatch3_LPS_B_Nr.19.CEL.gz
| | Sample_series_id | GSE42660
| | Sample_data_row_count | 54675
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