Search results for the GEO ID: GSE28237  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM699068 | GPL1261 |
|
T cell dependent immune responses: B cell activation and differentiation Group1 follicular B cells (Fo), Chip 2
|
B cell subsets
|
strain: BALB/c
gender: female
tissue: Spleen
cell type: follicular B cells (Fo)
|
Gene expression profiles of (a) Fo, (b) GC1, and (c) GC2 B cells prepared from the spleen of BALB/c mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2.
|
| Sample_geo_accession | GSM699068
| | Sample_status | Public on Mar 29 2011
| | Sample_submission_date | Mar 29 2011
| | Sample_last_update_date | Mar 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the spleen of BALB/c mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_growth_protocol_ch1 | Follicular B cells (B220+CD21intCD231 +) and germinal center B cells (B220+PNAhigh) were sorted to high purity (>99%) using FACS Aria (BD Bioscience). Follicular B cells were sorted from the spleen of non-immunized BALB/c mice, germinal center B cells 7 days (early germinal center B cells) or 15 days (late germinal center B cells) after immunization with the T cell dependent antigen 2-phenyl Oxazolone coupled to the carrier chicken serum albumin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All two chips of one group were compared to any of the two chips of the second group (4 comparisons between two groups) and all chips were additionally compared within each group, (2 comparisons in both directions within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal Increase, MI; Decrease, D; Marginal Decrease, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – four different t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 4 SLR values of group 1 vs. group 2 and 2 plus 2 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.38578E-07) or (b) more than 50% of non parametrically calculated Change calls (call after calculation of p value with Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria (for up- and down regulated genes separately); these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips, validated with the Affymetrix Latin Square dataset (accessible via public login without registration in the public data sets SGU of Bioretis) and compared successfully to Significance Analysis of Microarrays (SAM) and dChip in Menssen et al., 2009. Advantage of High Performance Chip Data Analysis (HPCDA) is amongst others the possibility to use always the same (default) parameters for all different datasets resulting in approx. 65 (Latin Square data set) up to 10,000 significant differentially regulated genes without parameter adjusting of the user.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699068/suppl/GSM699068.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699068/suppl/GSM699068.CHP.gz
| | Sample_series_id | GSE28237
| | Sample_data_row_count | 45101
| | |
|
GSM699069 | GPL1261 |
|
T cell dependent immune responses: B cell activation and differentiation Group1 follicular B cells (Fo), Chip 3
|
B cell subsets
|
strain: BALB/c
gender: female
tissue: Spleen
cell type: follicular B cells (Fo)
|
Gene expression profiles of (a) Fo, (b) GC1, and (c) GC2 B cells prepared from the spleen of BALB/c mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2.
|
| Sample_geo_accession | GSM699069
| | Sample_status | Public on Mar 29 2011
| | Sample_submission_date | Mar 29 2011
| | Sample_last_update_date | Mar 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the spleen of BALB/c mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_growth_protocol_ch1 | Follicular B cells (B220+CD21intCD231 +) and germinal center B cells (B220+PNAhigh) were sorted to high purity (>99%) using FACS Aria (BD Bioscience). Follicular B cells were sorted from the spleen of non-immunized BALB/c mice, germinal center B cells 7 days (early germinal center B cells) or 15 days (late germinal center B cells) after immunization with the T cell dependent antigen 2-phenyl Oxazolone coupled to the carrier chicken serum albumin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All two chips of one group were compared to any of the two chips of the second group (4 comparisons between two groups) and all chips were additionally compared within each group, (2 comparisons in both directions within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal Increase, MI; Decrease, D; Marginal Decrease, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – four different t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 4 SLR values of group 1 vs. group 2 and 2 plus 2 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.38578E-07) or (b) more than 50% of non parametrically calculated Change calls (call after calculation of p value with Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria (for up- and down regulated genes separately); these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips, validated with the Affymetrix Latin Square dataset (accessible via public login without registration in the public data sets SGU of Bioretis) and compared successfully to Significance Analysis of Microarrays (SAM) and dChip in Menssen et al., 2009. Advantage of High Performance Chip Data Analysis (HPCDA) is amongst others the possibility to use always the same (default) parameters for all different datasets resulting in approx. 65 (Latin Square data set) up to 10,000 significant differentially regulated genes without parameter adjusting of the user.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699069/suppl/GSM699069.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699069/suppl/GSM699069.CHP.gz
| | Sample_series_id | GSE28237
| | Sample_data_row_count | 45101
| | |
|
GSM699071 | GPL1261 |
|
T cell dependent immune responses: B cell activation and differentiation Group2 early germinal center Bcells (GC1) Chip2
|
B cell subsets
|
strain: BALB/c
gender: female
tissue: Spleen
cell type: early germinal center Bcells (GC1)
|
Gene expression profiles of (a) Fo, (b) GC1, and (c) GC2 B cells prepared from the spleen of BALB/c mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2.
|
| Sample_geo_accession | GSM699071
| | Sample_status | Public on Mar 29 2011
| | Sample_submission_date | Mar 29 2011
| | Sample_last_update_date | Mar 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the spleen of BALB/c mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_growth_protocol_ch1 | Follicular B cells (B220+CD21intCD231 +) and germinal center B cells (B220+PNAhigh) were sorted to high purity (>99%) using FACS Aria (BD Bioscience). Follicular B cells were sorted from the spleen of non-immunized BALB/c mice, germinal center B cells 7 days (early germinal center B cells) or 15 days (late germinal center B cells) after immunization with the T cell dependent antigen 2-phenyl Oxazolone coupled to the carrier chicken serum albumin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All two chips of one group were compared to any of the two chips of the second group (4 comparisons between two groups) and all chips were additionally compared within each group, (2 comparisons in both directions within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal Increase, MI; Decrease, D; Marginal Decrease, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – four different t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 4 SLR values of group 1 vs. group 2 and 2 plus 2 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.38578E-07) or (b) more than 50% of non parametrically calculated Change calls (call after calculation of p value with Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria (for up- and down regulated genes separately); these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips, validated with the Affymetrix Latin Square dataset (accessible via public login without registration in the public data sets SGU of Bioretis) and compared successfully to Significance Analysis of Microarrays (SAM) and dChip in Menssen et al., 2009. Advantage of High Performance Chip Data Analysis (HPCDA) is amongst others the possibility to use always the same (default) parameters for all different datasets resulting in approx. 65 (Latin Square data set) up to 10,000 significant differentially regulated genes without parameter adjusting of the user.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699071/suppl/GSM699071.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699071/suppl/GSM699071.CHP.gz
| | Sample_series_id | GSE28237
| | Sample_data_row_count | 45101
| | |
|
GSM699072 | GPL1261 |
|
T cell dependent immune responses: B cell activation and differentiation Group3 late germinal center B cell (GC2) Chip1
|
B cell subsets
|
strain: BALB/c
gender: female
tissue: Spleen
cell type: late germinal center B cell (GC2)
|
Gene expression profiles of (a) Fo, (b) GC1, and (c) GC2 B cells prepared from the spleen of BALB/c mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2.
|
| Sample_geo_accession | GSM699072
| | Sample_status | Public on Mar 29 2011
| | Sample_submission_date | Mar 29 2011
| | Sample_last_update_date | Mar 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the spleen of BALB/c mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_growth_protocol_ch1 | Follicular B cells (B220+CD21intCD231 +) and germinal center B cells (B220+PNAhigh) were sorted to high purity (>99%) using FACS Aria (BD Bioscience). Follicular B cells were sorted from the spleen of non-immunized BALB/c mice, germinal center B cells 7 days (early germinal center B cells) or 15 days (late germinal center B cells) after immunization with the T cell dependent antigen 2-phenyl Oxazolone coupled to the carrier chicken serum albumin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All two chips of one group were compared to any of the two chips of the second group (4 comparisons between two groups) and all chips were additionally compared within each group, (2 comparisons in both directions within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal Increase, MI; Decrease, D; Marginal Decrease, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – four different t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 4 SLR values of group 1 vs. group 2 and 2 plus 2 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.38578E-07) or (b) more than 50% of non parametrically calculated Change calls (call after calculation of p value with Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria (for up- and down regulated genes separately); these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips, validated with the Affymetrix Latin Square dataset (accessible via public login without registration in the public data sets SGU of Bioretis) and compared successfully to Significance Analysis of Microarrays (SAM) and dChip in Menssen et al., 2009. Advantage of High Performance Chip Data Analysis (HPCDA) is amongst others the possibility to use always the same (default) parameters for all different datasets resulting in approx. 65 (Latin Square data set) up to 10,000 significant differentially regulated genes without parameter adjusting of the user.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699072/suppl/GSM699072.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699072/suppl/GSM699072.CHP.gz
| | Sample_series_id | GSE28237
| | Sample_data_row_count | 45101
| | |
|
GSM699073 | GPL1261 |
|
T cell dependent immune responses: B cell activation and differentiation Group3 late germinal center B cell (GC2) Chip2
|
B cell subsets
|
strain: BALB/c
gender: female
tissue: Spleen
cell type: late germinal center B cell (GC2)
|
Gene expression profiles of (a) Fo, (b) GC1, and (c) GC2 B cells prepared from the spleen of BALB/c mice were compared using Affymetrix MG430Av2 GeneChip arrays. After total RNA extraction, reverse transcription, cDNA extraction, the biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized in duplicates for each of the three groups to the GeneChip arrays. Group1: Fo, Group2: GC1, Group3: GC2.
|
| Sample_geo_accession | GSM699073
| | Sample_status | Public on Mar 29 2011
| | Sample_submission_date | Mar 29 2011
| | Sample_last_update_date | Mar 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from the spleen of BALB/c mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_growth_protocol_ch1 | Follicular B cells (B220+CD21intCD231 +) and germinal center B cells (B220+PNAhigh) were sorted to high purity (>99%) using FACS Aria (BD Bioscience). Follicular B cells were sorted from the spleen of non-immunized BALB/c mice, germinal center B cells 7 days (early germinal center B cells) or 15 days (late germinal center B cells) after immunization with the T cell dependent antigen 2-phenyl Oxazolone coupled to the carrier chicken serum albumin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instruction. The amount, purity, and integrity of RNA were assessed for each sample using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano LabChip and a NanoDrop ND-1000 spectrophotometer. Contaminating genomic DNA was removed by an on-column DNA digestion step (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. Briefly, after total RNA extraction, 100 ng of total RNA from each cell sample was reverse transcribed, cDNA was extracted, biotinylated cRNA was transcribed, fragmented, and 15 µg cRNA hybridized to the GeneChip arrays.
| | Sample_hyb_protocol | Labeling and hybridization of total RNA was performed using the GeneChip 3’ IVT Express Kit from Affymetrix according to the manufacturers instruction. The MG430Av2 GeneChip arrays were loaded with the hybridization cocktail, hybridized at 45 °C for 16 h in a hybridization oven 640 (Affymetrix), washed and stained with streptavidin-phycoerythrin using the Affymetrix GeneChip Fluidics Workstation 400.
| | Sample_scan_protocol | Arrays were scanned with an Affymetrix GeneChip Scanner 3000
| | Sample_data_processing | Data were analyzed according to High Performance Chip Data Analysis (HPCDA, unpublished - Joachim R. Gruen) with the Bioretis database (http://www.bioretis-analysis.de/) using the default filter parameters for decreased and increased gene lists (description of database c.f. open access paper Menssen et al., 2009; PubMedID: 19265543). Chip data included in the Bioretis database were analyzed using the GeneChip Operating Software (GCOS, Affymetrix), version 1.4. Microarrays were globally normalized and scaled to a trimmed mean expression value of 150. Quality checks were performed according to the manufacturer's recommendations. All two chips of one group were compared to any of the two chips of the second group (4 comparisons between two groups) and all chips were additionally compared within each group, (2 comparisons in both directions within each group). The following parameters of absolute and comparative analysis were included in the Bioretis database: expression heights (Signals) and mean, median and standard deviation of Signals of both groups, call for presence of transcripts (Absent, A; Marginal, M; Present, P), p value for presence or absence of transcripts, log2 value of fold change (Signal Log Ratio, SLR) and the calculated fold change as mean values, call for the significance of differentially expression (Change Call: Increase, I; Marginal Increase, MI; Decrease, D; Marginal Decrease, MD; No Change, NC), and the p value for that call. Additionally – not with GCOS calculated – four different t tests of log Signals and SLRs were included in the database. For each present transcript the significance of differential expression between the groups of arrays was either calculated using (a) strict Bonferroni corrected Welch t tests between 4 SLR values of group 1 vs. group 2 and 2 plus 2 SLR values within both groups (the latter 4 giving a mean SLR value of zero; p-value had to be <= 1.38578E-07) or (b) more than 50% of non parametrically calculated Change calls (call after calculation of p value with Mann-Whitney U test, GCOS) i.e. 3 or more of all 4 Change calls have to be in the same direction. Significantly differentially expressed genes were filtered using the both default parameter sets of filter criteria (for up- and down regulated genes separately); these are a combination of four different queries. Filter criteria were developed with various data sets of GeneChips, validated with the Affymetrix Latin Square dataset (accessible via public login without registration in the public data sets SGU of Bioretis) and compared successfully to Significance Analysis of Microarrays (SAM) and dChip in Menssen et al., 2009. Advantage of High Performance Chip Data Analysis (HPCDA) is amongst others the possibility to use always the same (default) parameters for all different datasets resulting in approx. 65 (Latin Square data set) up to 10,000 significant differentially regulated genes without parameter adjusting of the user.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Joachim,R.,Grün
| | Sample_contact_email | Gruen@DRFZ.de
| | Sample_contact_department | Bioinformatics
| | Sample_contact_institute | Deutsches Rheuma-Forschungszentrum (DRFZ)
| | Sample_contact_address | Charitéplatz 1
| | Sample_contact_city | Berlin
| | Sample_contact_zip/postal_code | D-10117
| | Sample_contact_country | Germany
| | Sample_contact_web_link | www.drfz.de
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699073/suppl/GSM699073.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM699nnn/GSM699073/suppl/GSM699073.CHP.gz
| | Sample_series_id | GSE28237
| | Sample_data_row_count | 45101
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