Search results for the GEO ID: GSE20033  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM500988 | GPL570 |
|
H13_GSM378819
|
Human Embryonic Stem Cells
|
cell type: Human Embryonic Stem Cells
developmental stage: undifferentiated
|
GSM378819.CEL
|
| Sample_geo_accession | GSM500988
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500988/suppl/GSM500988.CEL.gz
| | Sample_relation | Reanalysis of: GSM378819
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM500990 | GPL570 |
|
H14_GSM378820
|
Human Embryonic Stem Cells
|
cell type: Human Embryonic Stem Cells
developmental stage: undifferentiated
|
GSM378820.CEL
|
| Sample_geo_accession | GSM500990
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500990/suppl/GSM500990.CEL.gz
| | Sample_relation | Reanalysis of: GSM378820
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM500992 | GPL570 |
|
H7_GSM378817
|
Human Embryonic Stem Cells
|
cell type: Human Embryonic Stem Cells
developmental stage: undifferentiated
|
GSM378817.CEL
|
| Sample_geo_accession | GSM500992
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500992/suppl/GSM500992.CEL.gz
| | Sample_relation | Reanalysis of: GSM378817
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM500994 | GPL570 |
|
H9_GSM378818
|
Human Embryonic Stem Cells
|
cell type: Human Embryonic Stem Cells
developmental stage: undifferentiated
|
GSM378818.CEL
|
| Sample_geo_accession | GSM500994
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Jan 27 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells (GM03813 and GM03814, Coriell Inst.) were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500994/suppl/GSM500994.CEL.gz
| | Sample_relation | Reanalysis of: GSM378818
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM500995 | GPL570 |
|
Foreskin_GSM378832
|
Foreskin Cells Parental
|
cell type: Foreskin Cells Parental
developmental stage: adult
|
GSM378832.CEL
|
| Sample_geo_accession | GSM500995
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500995/suppl/GSM500995.CEL.gz
| | Sample_relation | Reanalysis of: GSM378832
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM500996 | GPL570 |
|
JT-iPSC_GSM378833
|
iPS cells from episomal vectors (Defined Factor)
|
cell type: iPS cells from episomal vectors (Defined Factor)
developmental stage: undifferentiated
|
GSM378833.CEL
|
| Sample_geo_accession | GSM500996
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500996/suppl/GSM500996.CEL.gz
| | Sample_relation | Reanalysis of: GSM378833
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM500997 | GPL570 |
|
JT-iPSC_GSM378834
|
iPS cells from episomal vectors (Defined Factor sub-clone)
|
cell type: iPS cells from episomal vectors (Defined Factor sub-clone)
developmental stage: undifferentiated
|
GSM378834.CEL
|
| Sample_geo_accession | GSM500997
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500997/suppl/GSM500997.CEL.gz
| | Sample_relation | Reanalysis of: GSM378834
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM500998 | GPL570 |
|
JT-iPSC_GSM378836
|
iPS cells from episomal vectors (Defined Factor sub-clone)
|
cell type: iPS cells from episomal vectors (Defined Factor sub-clone)
developmental stage: undifferentiated
|
GSM378836.CEL
|
| Sample_geo_accession | GSM500998
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500998/suppl/GSM500998.CEL.gz
| | Sample_relation | Reanalysis of: GSM378836
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM500999 | GPL570 |
|
JT-iPSC_GSM378837
|
iPS cells from episomal vectors (Defined Factor sub-clone)
|
cell type: iPS cells from episomal vectors (Defined Factor sub-clone)
developmental stage: undifferentiated
|
GSM378837.CEL
|
| Sample_geo_accession | GSM500999
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM500nnn/GSM500999/suppl/GSM500999.CEL.gz
| | Sample_relation | Reanalysis of: GSM378837
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501000 | GPL570 |
|
JT-iPSC_GSM378838
|
iPS cells from episomal vectors (Defined Factor)
|
cell type: iPS cells from episomal vectors (Defined Factor)
developmental stage: undifferentiated
|
GSM378838.CEL
|
| Sample_geo_accession | GSM501000
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | iPS cells were maintained on irradiated mouse embryonic fibroblasts (MEF) as previously described. Fibroblast cells were cultured in Minimum Essential Medium (Eagle) (Invitrogen) supplemented with 10% heat-inactivated fetal bovine serum (HyClone Laboratories).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501000/suppl/GSM501000.CEL.gz
| | Sample_relation | Reanalysis of: GSM378838
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501001 | GPL570 |
|
human adipose stem cell replicate 1
|
adipose stem cells derived from adult human donor
|
cell type: adipose stem cells derived from adult human donor
developmental stage: undifferentiated
|
hASC_1.CEL
|
| Sample_geo_accession | GSM501001
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501001/suppl/GSM501001.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501002 | GPL570 |
|
human adipose stem cell replicate 2
|
adipose stem cells derived from adult human donor
|
cell type: adipose stem cells derived from adult human donor
developmental stage: adult
|
hASC_2.CEL
|
| Sample_geo_accession | GSM501002
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501002/suppl/GSM501002.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501003 | GPL570 |
|
human adipose stem cell replicate 3
|
adipose stem cells derived from adult human donor
|
cell type: adipose stem cells derived from adult human donor
developmental stage: adult
|
hASC_3.CEL
|
| Sample_geo_accession | GSM501003
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501003/suppl/GSM501003.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501004 | GPL570 |
|
hASC-derived iPS cells using lentiviral factors replicate 1
|
iPSC derived from hASC using lentiviral reprogramming vector
|
cell type: iPSC derived from hASC using lentiviral reprogramming vector
developmental stage: undifferentiated
|
lenti_hASC_iPS1.CEL
|
| Sample_geo_accession | GSM501004
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501004/suppl/GSM501004.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501005 | GPL570 |
|
hASC-derived iPS cells using lentiviral factors replicate 2
|
iPSC derived from hASC using lentiviral reprogramming vector
|
cell type: iPSC derived from hASC using lentiviral reprogramming vector
developmental stage: undifferentiated
|
lenti_hASC_iPS2.CEL
|
| Sample_geo_accession | GSM501005
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501005/suppl/GSM501005.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501006 | GPL570 |
|
hASC-derived iPS cells using lentiviral factors replicate 3
|
iPSC derived from hASC using lentiviral reprogramming vector
|
cell type: iPSC derived from hASC using lentiviral reprogramming vector
developmental stage: undifferentiated
|
lenti_hASC_iPS3.CEL
|
| Sample_geo_accession | GSM501006
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501006/suppl/GSM501006.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501007 | GPL570 |
|
minicircle-derived iPSC subclone 1
|
iPSC derived from hASC using minicircle reprogramming vector
|
cell type: iPSC derived from hASC using minicircle reprogramming vector
developmental stage: undifferentiated
|
minicircle_iPS1.CEL
|
| Sample_geo_accession | GSM501007
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501007/suppl/GSM501007.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501008 | GPL570 |
|
minicircle-derived iPSC subclone 2
|
iPSC derived from hASC using minicircle reprogramming vector
|
cell type: iPSC derived from hASC using minicircle reprogramming vector
developmental stage: undifferentiated
|
minicircle_iPS2.CEL
|
| Sample_geo_accession | GSM501008
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501008/suppl/GSM501008.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
GSM501009 | GPL570 |
|
minicircle-derived iPSC subclone 3
|
iPSC derived from hASC using minicircle reprogramming vector
|
cell type: iPSC derived from hASC using minicircle reprogramming vector
developmental stage: undifferentiated
|
minicircle_iPS3.CEL
|
| Sample_geo_accession | GSM501009
| | Sample_status | Public on Feb 01 2010
| | Sample_submission_date | Jan 25 2010
| | Sample_last_update_date | Aug 15 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Undifferentiated cells were cultured on Matrigel-coated (ES qualified; BD Biosciences) tissue culture dishes with mTESR-1 human ES Growth Medium (StemCell Technologies). hASCs were maintained with Dulbecco's Modified Eagle Medium (DMEM) containing 10% FBS, Glutamax-I, 4.5 g l–1 glucose, 110 mg l–1 sodium pyruvate, 50 units ml–1 penicillin and 50 µg ml–1 streptomycin at 37 °C, 95% air and 5% CO2 in a humidified incubator. All cells used for reprogramming were within passage 2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared using RNeasy Mini Kit (Qiagen)
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylated aRNA was prepared according to the protocol for GeneChip 3’ IVT Express Kit, Revision 7.
| | Sample_hyb_protocol | Following fragmentation, aRNA was hybridized on GeneChip Human Genome Array in a GeneChip Hybridization Oven 640.
| | Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner 3000 7G.
| | Sample_data_processing | The data were analyzed with AGCC (Affymetrix Genechip Command Console).
| | Sample_data_processing | Gene-level signal estimates were derived from the CEL files using GeneSpring GX 10.0 software. Summarization of gene expression data was performed by implementing the robust multichip averaging algorithm, with subsequent baseline normalization of the log-summarized values for each probe set to that of the median log summarized value for the same probe set in the control group. Expression data were then filtered to remove probe sets for which the signal intensities for all the treatment groups were in the lowest 20 percentile of all intensity values.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Kitchener,D.,Wilson
| | Sample_contact_email | kitchwilson@stanford.edu
| | Sample_contact_institute | Stanford University
| | Sample_contact_address | S140 Grant Bldg
| | Sample_contact_city | Stanford
| | Sample_contact_state | CA
| | Sample_contact_zip/postal_code | 94305
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM501nnn/GSM501009/suppl/GSM501009.CEL.gz
| | Sample_relation | Reanalyzed by: GSE49910
| | Sample_series_id | GSE20033
| | Sample_data_row_count | 49054
| | |
|
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