Search results for the GEO ID: GSE24437  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM602153 | GPL1261 |
|
Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group1 Hopx-/- Chip3
|
Hopx-/- Th1 cells in comparison to Hopx-expressing (Hopx+/- and Hopx+/+) Th cells
|
genotype/variation: Hopx-/-
strain: C57Bl6/OT2
gender: Male
tissue: spleen
cell type: Th1 effector memory cells
|
Gene expression profiles of (a) Hopx-/-, (b) Hopx+/-, and (c) Hopx+/+ Th1 cells generated from TcR-transgenic OT2 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: Hopx-/-, Group2: Hopx+/-, Group3: Hopx+/+.
|
| Sample_geo_accession | GSM602153
| | Sample_status | Public on Sep 30 2010
| | Sample_submission_date | Sep 29 2010
| | Sample_last_update_date | Sep 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from in vitro Th1 cultures generated from Hopx-deficient or Hopx-competent TcR-transgenic OT2 mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | Sample_growth_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | 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 for two samples per group, 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. 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_hyb_protocol | 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 for two samples per group, 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. 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 processing
| | 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 a 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 I, MI; Decrease, D; Marginal D, 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 and compared to Significance Analysis of Microarrays (SAM) and dChip as shown in Menssen et al., 2009; PubMedID: 19265543.
| | 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/GSM602nnn/GSM602153/suppl/GSM602153.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM602nnn/GSM602153/suppl/GSM602153.CHP.gz
| | Sample_series_id | GSE24437
| | Sample_data_row_count | 45101
| | |
|
GSM602159 | GPL1261 |
|
Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group1 Hopx-/- Chip4
|
Hopx-/- Th1 cells in comparison to Hopx-expressing (Hopx+/- and Hopx+/+) Th cells
|
genotype/variation: Hopx-/-
strain: C57Bl6/OT2
gender: Male
tissue: spleen
cell type: Th1 effector memory cells
|
Gene expression profiles of (a) Hopx-/-, (b) Hopx+/-, and (c) Hopx+/+ Th1 cells generated from TcR-transgenic OT2 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: Hopx-/-, Group2: Hopx+/-, Group3: Hopx+/+.
|
| Sample_geo_accession | GSM602159
| | Sample_status | Public on Sep 30 2010
| | Sample_submission_date | Sep 29 2010
| | Sample_last_update_date | Sep 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from in vitro Th1 cultures generated from Hopx-deficient or Hopx-competent TcR-transgenic OT2 mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | Sample_growth_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | 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 for two samples per group, 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. 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_hyb_protocol | 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 for two samples per group, 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. 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 processing
| | 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 a 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 I, MI; Decrease, D; Marginal D, 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 and compared to Significance Analysis of Microarrays (SAM) and dChip as shown in Menssen et al., 2009; PubMedID: 19265543.
| | 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/GSM602nnn/GSM602159/suppl/GSM602159.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM602nnn/GSM602159/suppl/GSM602159.CHP.gz
| | Sample_series_id | GSE24437
| | Sample_data_row_count | 45101
| | |
|
GSM602160 | GPL1261 |
|
Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group2 Hopx+/- Chip3
|
Hopx-/- Th1 cells in comparison to Hopx-expressing (Hopx+/- and Hopx+/+) Th cells
|
genotype/variation: Hopx+/-
strain: C57Bl6/OT2
gender: Male
tissue: spleen
cell type: Th1 effector memory cells
|
Gene expression profiles of (a) Hopx-/-, (b) Hopx+/-, and (c) Hopx+/+ Th1 cells generated from TcR-transgenic OT2 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: Hopx-/-, Group2: Hopx+/-, Group3: Hopx+/+.
|
| Sample_geo_accession | GSM602160
| | Sample_status | Public on Sep 30 2010
| | Sample_submission_date | Sep 29 2010
| | Sample_last_update_date | Sep 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from in vitro Th1 cultures generated from Hopx-deficient or Hopx-competent TcR-transgenic OT2 mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | Sample_growth_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | 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 for two samples per group, 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. 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_hyb_protocol | 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 for two samples per group, 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. 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 processing
| | 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 a 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 I, MI; Decrease, D; Marginal D, 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 and compared to Significance Analysis of Microarrays (SAM) and dChip as shown in Menssen et al., 2009; PubMedID: 19265543.
| | 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/GSM602nnn/GSM602160/suppl/GSM602160.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM602nnn/GSM602160/suppl/GSM602160.CHP.gz
| | Sample_series_id | GSE24437
| | Sample_data_row_count | 45101
| | |
|
GSM602162 | GPL1261 |
|
Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group2 Hopx+/- Chip4
|
Hopx-/- Th1 cells in comparison to Hopx-expressing (Hopx+/- and Hopx+/+) Th cells
|
genotype/variation: Hopx+/-
strain: C57Bl6/OT2
gender: Male
tissue: spleen
cell type: Th1 effector memory cells
|
Gene expression profiles of (a) Hopx-/-, (b) Hopx+/-, and (c) Hopx+/+ Th1 cells generated from TcR-transgenic OT2 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: Hopx-/-, Group2: Hopx+/-, Group3: Hopx+/+.
|
| Sample_geo_accession | GSM602162
| | Sample_status | Public on Sep 30 2010
| | Sample_submission_date | Sep 29 2010
| | Sample_last_update_date | Sep 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from in vitro Th1 cultures generated from Hopx-deficient or Hopx-competent TcR-transgenic OT2 mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | Sample_growth_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | 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 for two samples per group, 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. 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_hyb_protocol | 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 for two samples per group, 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. 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 processing
| | 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 a 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 I, MI; Decrease, D; Marginal D, 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 and compared to Significance Analysis of Microarrays (SAM) and dChip as shown in Menssen et al., 2009; PubMedID: 19265543.
| | 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/GSM602nnn/GSM602162/suppl/GSM602162.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM602nnn/GSM602162/suppl/GSM602162.CHP.gz
| | Sample_series_id | GSE24437
| | Sample_data_row_count | 45101
| | |
|
GSM602163 | GPL1261 |
|
Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group3 Hopx+/+ Chip3
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Hopx-/- Th1 cells in comparison to Hopx-expressing (Hopx+/- and Hopx+/+) Th cells
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genotype/variation: Hopx+/+
strain: C57Bl6/OT2
gender: Male
tissue: spleen
cell type: Th1 effector memory cells
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Gene expression profiles of (a) Hopx-/-, (b) Hopx+/-, and (c) Hopx+/+ Th1 cells generated from TcR-transgenic OT2 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: Hopx-/-, Group2: Hopx+/-, Group3: Hopx+/+.
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| Sample_geo_accession | GSM602163
| | Sample_status | Public on Sep 30 2010
| | Sample_submission_date | Sep 29 2010
| | Sample_last_update_date | Sep 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from in vitro Th1 cultures generated from Hopx-deficient or Hopx-competent TcR-transgenic OT2 mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | Sample_growth_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | 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 for two samples per group, 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. 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_hyb_protocol | 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 for two samples per group, 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. 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 processing
| | 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 a 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 I, MI; Decrease, D; Marginal D, 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 and compared to Significance Analysis of Microarrays (SAM) and dChip as shown in Menssen et al., 2009; PubMedID: 19265543.
| | 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/GSM602nnn/GSM602163/suppl/GSM602163.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM602nnn/GSM602163/suppl/GSM602163.CHP.gz
| | Sample_series_id | GSE24437
| | Sample_data_row_count | 45101
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GSM602183 | GPL1261 |
|
Persistence of effector memory Th1 cells is regulated by the homeobox only protein Group3 Hopx+/+ Chip4
|
Hopx-/- Th1 cells in comparison to Hopx-expressing (Hopx+/- and Hopx+/+) Th cells
|
genotype/variation: Hopx+/+
strain: C57Bl6/OT2
gender: Male
tissue: spleen
cell type: Th1 effector memory cells
|
Gene expression profiles of (a) Hopx-/-, (b) Hopx+/-, and (c) Hopx+/+ Th1 cells generated from TcR-transgenic OT2 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: Hopx-/-, Group2: Hopx+/-, Group3: Hopx+/+.
|
| Sample_geo_accession | GSM602183
| | Sample_status | Public on Sep 30 2010
| | Sample_submission_date | Sep 29 2010
| | Sample_last_update_date | Sep 29 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Samples were obtained from in vitro Th1 cultures generated from Hopx-deficient or Hopx-competent TcR-transgenic OT2 mice (DRFZ, Marienfelde, Berlin, Germany)
| | Sample_treatment_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | Sample_growth_protocol_ch1 | Naïve Th cells were isolated from Hopx-/-, Hopx+/- and Hopx+/+ OT2 mice and activated for 6 days with Ova peptide, APCs and IL-12 where the latter favors a polarization into Th1 cells. Viable cells were isolated by Ficoll Histopaque density gradient centrifugation and again activated with Ova, APCs, IL-12 and IL-2 for another period of 6 days. On day 12, again viable cells were isolated by Ficoll Histopaque density gradient centrifugation and their transcriptomes were subsequently analyzed.
| | 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 for two samples per group, 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. 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_hyb_protocol | 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 for two samples per group, 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. 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 processing
| | 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 a 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 I, MI; Decrease, D; Marginal D, 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 and compared to Significance Analysis of Microarrays (SAM) and dChip as shown in Menssen et al., 2009; PubMedID: 19265543.
| | 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/GSM602nnn/GSM602183/suppl/GSM602183.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM602nnn/GSM602183/suppl/GSM602183.CHP.gz
| | Sample_series_id | GSE24437
| | Sample_data_row_count | 45101
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