Search results for the GEO ID: GSE43956  |
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GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1075005 | GPL1261 |
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WT-IL23 rep1
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Th17 cells
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genotype: WT
cell type: Th17
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| Sample_geo_accession | GSM1075005
| | Sample_status | Public on Mar 07 2013
| | Sample_submission_date | Jan 31 2013
| | Sample_last_update_date | Mar 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). After differentiation, the cells were then rested for 72 h and restimulated with IL-23
| | Sample_growth_protocol_ch1 | Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. 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 | Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Nir,,Yosef
| | Sample_contact_email | nir@broadinstitute.org
| | Sample_contact_phone | (617) 714-7734
| | Sample_contact_laboratory | Regev
| | Sample_contact_institute | Broad
| | Sample_contact_address | 7 Cambridge center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.broadinstitute.org/~nir/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1075nnn/GSM1075005/suppl/GSM1075005_sample_5_1781G.CEL.gz
| | Sample_series_id | GSE43956
| | Sample_series_id | GSE43970
| | Sample_data_row_count | 45101
| | |
|
GSM1075006 | GPL1261 |
|
WT-IL23 rep2
|
Th17 cells
|
genotype: WT
cell type: Th17
|
|
| Sample_geo_accession | GSM1075006
| | Sample_status | Public on Mar 07 2013
| | Sample_submission_date | Jan 31 2013
| | Sample_last_update_date | Mar 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). After differentiation, the cells were then rested for 72 h and restimulated with IL-23
| | Sample_growth_protocol_ch1 | Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. 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 | Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Nir,,Yosef
| | Sample_contact_email | nir@broadinstitute.org
| | Sample_contact_phone | (617) 714-7734
| | Sample_contact_laboratory | Regev
| | Sample_contact_institute | Broad
| | Sample_contact_address | 7 Cambridge center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.broadinstitute.org/~nir/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1075nnn/GSM1075006/suppl/GSM1075006_sample_6_1781H.CEL.gz
| | Sample_series_id | GSE43956
| | Sample_series_id | GSE43970
| | Sample_data_row_count | 45101
| | |
|
GSM1075007 | GPL1261 |
|
SGK1-IL23 rep1
|
Th17 cells
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genotype: Sgk1-/-
cell type: Th17
|
|
| Sample_geo_accession | GSM1075007
| | Sample_status | Public on Mar 07 2013
| | Sample_submission_date | Jan 31 2013
| | Sample_last_update_date | Mar 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). After differentiation, the cells were then rested for 72 h and restimulated with IL-23
| | Sample_growth_protocol_ch1 | Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. 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 | Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Nir,,Yosef
| | Sample_contact_email | nir@broadinstitute.org
| | Sample_contact_phone | (617) 714-7734
| | Sample_contact_laboratory | Regev
| | Sample_contact_institute | Broad
| | Sample_contact_address | 7 Cambridge center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.broadinstitute.org/~nir/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1075nnn/GSM1075007/suppl/GSM1075007_sample_7_1781C.CEL.gz
| | Sample_series_id | GSE43956
| | Sample_series_id | GSE43970
| | Sample_data_row_count | 45101
| | |
|
GSM1075008 | GPL1261 |
|
SGK1-IL23 rep2
|
Th17 cells
|
genotype: Sgk1-/-
cell type: Th17
|
|
| Sample_geo_accession | GSM1075008
| | Sample_status | Public on Mar 07 2013
| | Sample_submission_date | Jan 31 2013
| | Sample_last_update_date | Mar 07 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | For Th17 differentiation: 2ng/mL rhTGF-β1 (Miltenyi Biotec), 25ng/mL rmIl-6 (Miltenyi Biotec), 20ng/ml rmIl-23 (Miltenyi Biotec), and 20ng/ml rmIL-β1 (Miltenyi Biotec). After differentiation, the cells were then rested for 72 h and restimulated with IL-23
| | Sample_growth_protocol_ch1 | Cd4+ T cells were purified from spleen and lymph nodes using anti-CD4 microbeads (Miltenyi Biotech) then stained in PBS with 1% FCS for 20 min at room temperature with anti-Cd4-PerCP, anti-Cd62l-APC, and anti-Cd44-PE antibodies (all Biolegend, CA). Naïve Cd4+ Cd62lhigh Cd44low T cells were sorted using the BD FACSAria cell sorter. Sorted cells were activated with plate bound anti-Cd3 (2μg/ml) and anti-Cd28 (2μg/ml) in the presence of cytokines.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA (3' IVT Express Kit, Affymetrix).
| | Sample_hyb_protocol | Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Mouse 430 2.0 microarrays. 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 | Expression data was preprocessed using the RMA algorithm followed by quantile normalization, with the parameters in the ExpressionFileCreator module of the GenePattern suite set to default
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Nir,,Yosef
| | Sample_contact_email | nir@broadinstitute.org
| | Sample_contact_phone | (617) 714-7734
| | Sample_contact_laboratory | Regev
| | Sample_contact_institute | Broad
| | Sample_contact_address | 7 Cambridge center
| | Sample_contact_city | Cambridge
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02142
| | Sample_contact_country | USA
| | Sample_contact_web_link | http://www.broadinstitute.org/~nir/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1075nnn/GSM1075008/suppl/GSM1075008_sample_8_1781D_RR1.CEL.gz
| | Sample_series_id | GSE43956
| | Sample_series_id | GSE43970
| | Sample_data_row_count | 45101
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