Search results for the GEO ID: GSE13235  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM325720 | GPL1261 |
|
D3-pOct4 (pass 31) with LIF
|
D3-pOct4 mouse embryonic stem cells with LIF
|
D3-pOct4 treated with LIF, replicate 1
|
D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 1
|
| Sample_geo_accession | GSM325720
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Sep 30 2008
| | Sample_last_update_date | Nov 24 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | The undifferentiated state of the cells was maintained by adding of 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding of 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were cultured as basal condition. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM of sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325720/suppl/GSM325720.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325720/suppl/GSM325720.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
|
GSM325775 | GPL1261 |
|
D3-pOct4 (pass 31) without LIF
|
D3-pOct4 mouse embryonic stem cells without LIF
|
D3-pOct4 treated without LIF, replicate 1
|
D3-pOct4 cells cultured in the absence of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 1
|
| Sample_geo_accession | GSM325775
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Oct 01 2008
| | Sample_last_update_date | Oct 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325775/suppl/GSM325775.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325775/suppl/GSM325775.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
|
GSM325776 | GPL1261 |
|
D3-pOct4 (pass 31) without LIF plus NO
|
D3-pOct4 mouse embryonic stem cells without LIF plus NO
|
D3-pOct4 treated without LIF adding NO, replicate 1
|
D3-pOct4 cells cultured in the absence of LIF with 2µM of DETA/NO were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 1
|
| Sample_geo_accession | GSM325776
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Oct 01 2008
| | Sample_last_update_date | Oct 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325776/suppl/GSM325776.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325776/suppl/GSM325776.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
|
GSM325777 | GPL1261 |
|
D3-pOct4 (pass 33) with LIF
|
D3-pOct4 mouse embryonic stem cells with LIF
|
D3-pOct4 treated with LIF, replicate 2
|
D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 2
|
| Sample_geo_accession | GSM325777
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Oct 01 2008
| | Sample_last_update_date | Oct 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325777/suppl/GSM325777.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325777/suppl/GSM325777.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
|
GSM325778 | GPL1261 |
|
D3-pOct4 (pass 33) without LIF
|
D3-pOct4 mouse embryonic stem cells without LIF
|
D3-pOct4 treated without LIF, replicate 2
|
D3-pOct4 cells cultured in the absence of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 2
|
| Sample_geo_accession | GSM325778
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Oct 01 2008
| | Sample_last_update_date | Oct 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325778/suppl/GSM325778.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325778/suppl/GSM325778.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
|
GSM325779 | GPL1261 |
|
D3-pOct4 (pass 33) without LIF plus NO
|
D3-pOct4 mouse embryonic stem cells without LIF plus NO
|
D3-pOct4 treated without LIF adding NO, replicate 2
|
D3-pOct4 cells cultured in the absence of LIF with 2µM of DETA/NO were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 2
|
| Sample_geo_accession | GSM325779
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Oct 01 2008
| | Sample_last_update_date | Oct 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325779/suppl/GSM325779.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325779/suppl/GSM325779.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
|
GSM325780 | GPL1261 |
|
D3-pOct4 (pass 34) with LIF
|
D3-pOct4 mouse embryonic stem cells with LIF
|
D3-pOct4 treated with LIF, replicate 3
|
D3-pOct4 cells cultured in the presence of 1000 U/ml of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 3
|
| Sample_geo_accession | GSM325780
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Oct 01 2008
| | Sample_last_update_date | Oct 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_extract_protocol_ch1 |
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325780/suppl/GSM325780.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325780/suppl/GSM325780.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
|
GSM325783 | GPL1261 |
|
D3-pOct4 (pass 34) without LIF
|
D3-pOct4 mouse embryonic stem cells without LIF
|
D3-pOct4 treated without LIF, replicate 3
|
D3-pOct4 cells cultured in the absence of LIF were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 3
|
| Sample_geo_accession | GSM325783
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Oct 01 2008
| | Sample_last_update_date | Oct 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325783/suppl/GSM325783.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325783/suppl/GSM325783.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
|
GSM325784 | GPL1261 |
|
D3-pOct4 (pass 34) without LIF plus NO
|
D3-pOct4 mouse embryonic stem cells without LIF plus NO
|
D3-pOct4 treated without LIF adding NO, replicate 3
|
D3-pOct4 cells cultured in the absence of LIF with 2µM of DETA/NO were grown for 7 days, maintaining the conditions of the treatment everyday.
Replicate 3
|
| Sample_geo_accession | GSM325784
| | Sample_status | Public on Oct 17 2008
| | Sample_submission_date | Oct 01 2008
| | Sample_last_update_date | Oct 16 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_biomaterial_provider_ch1 | Cell line obtained from the Department of Cell Therapy and Regenerative Medicine in CABIMER
| | Sample_treatment_protocol_ch1 | For experiments, the undifferentiated state was maintained by adding 1000 U/ml of recombinant leukemia inhibitory factor (rLIF (Gibco)) to the culture medium. Cells treated with nitric oxide (NO) were maintained by adding 2µM of Diethylenetriamine/nitric oxide adduct (DETA/NO) to the culture medium without LIF. Cells without LIF were also cultured. All the cultures were maintained for 7 days.
| | Sample_growth_protocol_ch1 | The D3-pOct4 mESCs were cultured at low density in Dulbecco’s modified Eagle’s Medium (DMEM) (Gibco) supplemented with 15% fetal bovine serum (FBS) (Gibco), 1% of nonessential amino acids, 0.1 mM of 2-mercaptoethanol, 4 mM of L-glutamine, 1 mM sodium pyruvate, 100 IU/ml penicillin and 0.1 mg/ml streptomycin. Incubation at 37ºC and 5% CO2
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were recovered with trypsinization by 5 min at 37ºC. The pellets of cells were resuspended in Easy Blue reagent (Intron Biotechnology) for RNA extraction. The absorbance was checked at 260 and 280 nm for determination of sample concentration and purity. Integrity of total RNA samples were assessed qualitatively on an Agilent 2100 Bioanalyzer
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Biotinylated cRNA was prepared according to the standard Affymetrix protocol from 1.5 µg total RNA (Expression Analysis Technical Manual, 2004, Affymetrix). The products of reaction were purified and then fragmented at 94ºC during 35 min to obtain fragments between 35 and 200 bp.
| | Sample_hyb_protocol | Following fragmentation, 15 µg of cRNA were hybridized for 16 hr at 45ºC on GeneChip® Mouse Genome 430_2.0 (Affymetrix). GeneChips were washed and stained in the Affymetrix Fluidics Station FS450 according to the GeneChip® Expression Analysis Technical Manual, Affymetrix, 2004.
| | Sample_scan_protocol | Microarrays were scanned using the GeneChip® Scanner 3000 7G of Affymetrix.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings from GeneChip Operating System v1.4.0.036 and global scaling as the normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Rafael,A.,Tapia Limonchi
| | Sample_contact_email | rafael.tapia@cabimer.es
| | Sample_contact_phone | +34 954 467 840
| | Sample_contact_fax | +34 954 461 664
| | Sample_contact_laboratory | MR2
| | Sample_contact_department | Department of Cell Therapy and Regenerative Medicine
| | Sample_contact_institute | Andaluzian Center for Molecular Biology and Regenerative Medicine (CABIMER)
| | Sample_contact_address | Av. Américo Vespucio s/n-Edif. CABIMER Parque Científico y Tecnológico Cartuja 93
| | Sample_contact_city | Seville
| | Sample_contact_state | Seville
| | Sample_contact_zip/postal_code | 41092
| | Sample_contact_country | Spain
| | Sample_contact_web_link | http://www.cabimer.es/es/index.php?option=com_kgrupos&Itemid=63
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325784/suppl/GSM325784.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM325nnn/GSM325784/suppl/GSM325784.CHP.gz
| | Sample_series_id | GSE13235
| | Sample_data_row_count | 45101
| | |
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