Search results for the GEO ID: GSE42835 |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1051138 | GPL1261 |
|
liver WT iNKT cells rep 1
|
sorted iNKT cells from liver of WT mice
|
tissue: liver
age: 8 weeks old mice
strain: C57BL6N
treatment: no activation
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old C57BL6N mice
|
Sample_geo_accession | GSM1051138
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051138/suppl/GSM1051138_jos4068.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051139 | GPL1261 |
|
liver WT iNKT cells rep 2
|
sorted iNKT cells from liver of WT mice
|
tissue: liver
age: 8 weeks old mice
strain: C57BL6N
treatment: no activation
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old C57BL6N mice
|
Sample_geo_accession | GSM1051139
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051139/suppl/GSM1051139_jos4072.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051140 | GPL1261 |
|
liver WT iNKT cells rep 3
|
sorted iNKT cells from liver of WT mice
|
tissue: liver
age: 8 weeks old mice
strain: C57BL6N
treatment: no activation
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old C57BL6N mice
|
Sample_geo_accession | GSM1051140
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051140/suppl/GSM1051140_jos4076.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051141 | GPL1261 |
|
liver Tg iNKT cells rep 1
|
sorted iNKT cells from liver of Tg mice
|
tissue: liver
age: 8 weeks old mice
strain: pLck-hCD1dTg
treatment: no activation
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old pLck-hCD1d Tg mice
|
Sample_geo_accession | GSM1051141
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051141/suppl/GSM1051141_jos4069.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051142 | GPL1261 |
|
liver Tg iNKT cells rep 2
|
sorted iNKT cells from liver of Tg mice
|
tissue: liver
age: 8 weeks old mice
strain: pLck-hCD1dTg
treatment: no activation
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old pLck-hCD1d Tg mice
|
Sample_geo_accession | GSM1051142
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051142/suppl/GSM1051142_jos4073.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051143 | GPL1261 |
|
liver Tg iNKT cells rep 3
|
sorted iNKT cells from liver of Tg mice
|
tissue: liver
age: 8 weeks old mice
strain: pLck-hCD1dTg
treatment: no activation
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old pLck-hCD1d Tg mice
|
Sample_geo_accession | GSM1051143
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051143/suppl/GSM1051143_jos4077.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051144 | GPL1261 |
|
liver WT iNKT activated cells rep 1
|
sorted iNKT cells from liver of WT mice after 6 hs of in vitro activation
|
tissue: liver
age: 8 weeks old mice
strain: C57BL6N
treatment: activated in vitro for 6 hours
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old C57BL6N mice and activated in vitro for 6 hs
|
Sample_geo_accession | GSM1051144
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051144/suppl/GSM1051144_jos4070.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051145 | GPL1261 |
|
liver WT iNKT activated cells rep 2
|
sorted iNKT cells from liver of WT mice after 6 hs of in vitro activation
|
tissue: liver
age: 8 weeks old mice
strain: C57BL6N
treatment: activated in vitro for 6 hours
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old C57BL6N mice and activated in vitro for 6 hs
|
Sample_geo_accession | GSM1051145
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051145/suppl/GSM1051145_jos4074.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051146 | GPL1261 |
|
liver WT iNKT activated cells rep 3
|
sorted iNKT cells from liver of WT mice after 6 hs of in vitro activation
|
tissue: liver
age: 8 weeks old mice
strain: C57BL6N
treatment: activated in vitro for 6 hours
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old C57BL6N mice and activated in vitro for 6 hs
|
Sample_geo_accession | GSM1051146
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051146/suppl/GSM1051146_jos4078.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051147 | GPL1261 |
|
liver Tg iNKT activated cells rep 1
|
sorted iNKT cells from liver of Tg mice after 6 hs of in vitro activation
|
tissue: liver
age: 8 weeks old mice
strain: pLck-hCD1dTg
treatment: activated in vitro for 6 hours
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old pLck-hCD1d Tg mice and activated in vitro for 6 hs
|
Sample_geo_accession | GSM1051147
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051147/suppl/GSM1051147_jos4071.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051148 | GPL1261 |
|
liver Tg iNKT activated cells rep 2
|
sorted iNKT cells from liver of Tg mice after 6 hs of in vitro activation
|
tissue: liver
age: 8 weeks old mice
strain: pLck-hCD1dTg
treatment: activated in vitro for 6 hours
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old pLck-hCD1d Tg mice and activated in vitro for 6 hs
|
Sample_geo_accession | GSM1051148
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051148/suppl/GSM1051148_jos4075.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
GSM1051149 | GPL1261 |
|
liver Tg iNKT activated cells rep 3
|
sorted iNKT cells from liver of Tg mice after 6 hs of in vitro activation
|
tissue: liver
age: 8 weeks old mice
strain: pLck-hCD1dTg
treatment: activated in vitro for 6 hours
|
Gene expression data from iNKT cells sorted from liver of 8 weeks old pLck-hCD1d Tg mice and activated in vitro for 6 hs
|
Sample_geo_accession | GSM1051149
| Sample_status | Public on Mar 01 2013
| Sample_submission_date | Dec 10 2012
| Sample_last_update_date | Mar 01 2013
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Mus musculus
| Sample_taxid_ch1 | 10090
| Sample_treatment_protocol_ch1 | Ex vivo resting samples (rest) were kept at 4ºC and lysed immediately after sorting. In vitro activated samples (6hr-act) were lysed after 6 hours activation in vitro, by cross-linking the mCD1d-dimers bound to the TCR with plastic-bound goat anti-rat IgGs and costimulating with anti-CD28 mAb
| Sample_growth_protocol_ch1 | Highly purified peripheral iNKT cells ( aGalCer-mCD1dDimers+ TCRb+ CD19/I-Ab- cells) were obtained by flow-cytometric cell sorting from purified liver MNCs of B6 wt and pLck-hCD1d Tg mice the purity of the samples after sorting was tested and attained to > 90%
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA from 2-6x10^4 sorted iNKT cells for each sample was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | aRNA was biotin-labeled with BioArray High Yield RNA Transcription Labeling Kit (Enzo)
| Sample_hyb_protocol | Following fragmentation, 10 μg of cRNAs were hybridized to M430 2.0 chips (Affymetrix) for 16 h at 45°C with constant rotation at 60 rpm. Next, they were washed and conjugated with streptavidin-PE in the Fluidics Station 400 (Affymetrix).
| Sample_scan_protocol | Chips were scanned using on a GeneArray Scanner (Affymetrix).
| Sample_data_processing | The data were analyzed with the GenePattern software package (www.broad.mit.edu/cancer/software/genepattern/). Raw data were normalized by the RMA algorithm using the Expression File Creator module of GenePattern.
| Sample_platform_id | GPL1261
| Sample_contact_name | Giulia,,Casorati
| Sample_contact_email | casorati.giulia@hsr.it
| Sample_contact_phone | 0226434727
| Sample_contact_laboratory | Experimental Immunology Unit
| Sample_contact_department | Division of Immunology, Transplantation and Infectious Diseases
| Sample_contact_institute | San Raffaele Scientific Institute
| Sample_contact_address | Via Olgettina 58
| Sample_contact_city | Milan
| Sample_contact_state | Milan
| Sample_contact_zip/postal_code | 20132
| Sample_contact_country | Italy
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1051nnn/GSM1051149/suppl/GSM1051149_jos4079.CEL.gz
| Sample_series_id | GSE42835
| Sample_data_row_count | 45101
| |
|
|
|
Make groups for comparisons |
(2 groups will be compared at a time) |
|
Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|