Search results for the GEO ID: GSE18265  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM388581 | GPL570 |
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HESC_HD90_p8
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Human embryonic stem cell line HD90/FE07-142-L1, carrying a point mutation in the VHL gene
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cell line: HD90/FE07-142-L1
cell type: human embryonic stem cells
embryo characteristic: mutation in VHL gene
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This human embryonic stem cell line was derived on an irradiated human fibroblast feeder, in 20% KO-SR medium, from an embryo carrying a mutation in the VHL gene as evidence by preimplantation genetic diagnostic (PGD). RNA extraction was carried out at passage 8.
HD90 was compared to a compendium of 84 transcriptome covering a broad range of adult tissues and other human embryonic stem cell lines. Data can also be accessed at http://www.amazonia.transcriptome.eu.
|
| Sample_geo_accession | GSM388581
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Apr 01 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hESCs derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM388nnn/GSM388581/suppl/GSM388581.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM388nnn/GSM388581/suppl/GSM388581.CHP.gz
| | Sample_series_id | GSE15491
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
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GSM388636 | GPL570 |
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HESC_HD129_p6
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Human embryonic stem cell line HD129/FE08-005-L1 obtained from a cystic fibrosis embryo
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cell line: HD129/FE08-005-L1
cell type: human embryonic stem cells
embryo characteristic: cystic fibrosis
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This human embryonic stem cell line was derived on an irradiated human fibroblast feeder, in 20% KO-SR medium, from a cystic fibrosis embryo as evidenced by preimplantation genetic diagnostic (PGD). RNA extraction was carried out at p6.
HD129 was compared to a compendium of 84 transcriptome covering a broad range of adult tissues and other human embryonic stem cell lines.
|
| Sample_geo_accession | GSM388636
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Apr 01 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hESCs derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM388nnn/GSM388636/suppl/GSM388636.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM388nnn/GSM388636/suppl/GSM388636.CHP.gz
| | Sample_series_id | GSE15491
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
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GSM388638 | GPL570 |
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HESC_HD83_p24
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Human embryonic stem cell line HD83/FE07-135-L1
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cell line: HD83/FE07-135-L1
cell type: human embryonic stem cells
embryo characteristic: normal
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This human embryonic stem cell line was derived on irradiated human fibroblasts, in 20% KO-SR medium and 10 ng/ml bFGF, from a normal embryo. RNA extraction was carried out at p24.
HD83 was compared to a compendium of 84 transcriptome covering a broad range of adult tissues and other human embryonic stem cell lines.
|
| Sample_geo_accession | GSM388638
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Apr 01 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hESCs derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM388nnn/GSM388638/suppl/GSM388638.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM388nnn/GSM388638/suppl/GSM388638.CHP.gz
| | Sample_series_id | GSE15491
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
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GSM452261 | GPL570 |
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HESC HS235
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Human embryonic stem cell line HS235
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cell line: HS235 obtained from the Karolinska Instute of Stockholm, Sweden
cell type: human embryonic stem cells
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The hesc lines hs235 was derived by the team of Pr. Outi Hovatta at the Karolinska Institute (Stockholm, Sweden) and cultured on human foreskin fibroblast feeder cells (crl-2429; american type culture collection, manassas, va, http: //www. atcc.org) (Hovatta et al. 2003).
The transcriptome of this hESC was compared to the transcriptome of fully reprogrammed human induced pluripotent stem cells, the parental fibroblast cells and partially reprogrammed cells.
|
| Sample_geo_accession | GSM452261
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Oct 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hESCs culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452261/suppl/GSM452261.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452261/suppl/GSM452261.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM452297 | GPL570 |
|
Partially reprogrammed clone GRA_M5C1p3
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Partially reprogrammed human induced pluripotent stem cells clone GRA_M5C1p3
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clone: GRA_M5C1p3
cell type: partially reprogrammed human induced pluripotent stem cells
|
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Partially reprogrammed cells that displayed neither a fibroblast morphology nor a bona fide hiPS morphology were picked up and further expanded and characterized.
The transcriptome of partially reprogrammed cells was compared to the transcriptome of the parental fibroblast cells, fully reprogrammed human induced pluripotent stem cells and hESC.
|
| Sample_geo_accession | GSM452297
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hiPS derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452297/suppl/GSM452297.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452297/suppl/GSM452297.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM452298 | GPL570 |
|
Partially reprogrammed clone GRA_M5VC1p3
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Partially reprogrammed human induced pluripotent stem cells clone GRA_M5VC1p3
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clone: GRA_M5VC1p3
cell type: partially reprogrammed human induced pluripotent stem cells
|
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Partially reprogrammed cells that displayed neither a fibroblast morphology nor a bona fide hiPS morphology were picked up and further expanded and characterized.
The transcriptome of partially reprogrammed cells was compared to the transcriptome of the parental fibroblast cells, fully reprogrammed human induced pluripotent stem cells and hESC.
|
| Sample_geo_accession | GSM452298
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hiPS derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452298/suppl/GSM452298.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452298/suppl/GSM452298.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM452351 | GPL570 |
|
Partially reprogrammed clone INT_M4C1-1p5
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Partially reprogrammed human induced pluripotent stem cells clone INT_M4C1-1p5
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clone: INT_M4C1-1p5
cell type: partially reprogrammed human induced pluripotent stem cells
|
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Partially reprogrammed cells that displayed neither a fibroblast morphology nor a bona fide hiPS morphology were picked up and further expanded and characterized.
The transcriptome of partially reprogrammed cells was compared to the transcriptome of the parental fibroblast cells, fully reprogrammed human induced pluripotent stem cells and hESC.
|
| Sample_geo_accession | GSM452351
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hiPS derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452351/suppl/GSM452351.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452351/suppl/GSM452351.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM452352 | GPL570 |
|
Partially reprogrammed clone INT_M4C1p4
|
Partially reprogrammed human induced pluripotent stem cells clone INT_M4C1p4
|
clone: INT_M4C1p4
cell type: partially reprogrammed human induced pluripotent stem cells
|
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Partially reprogrammed cells that displayed neither a fibroblast morphology nor a bona fide hiPS morphology were picked up and further expanded and characterized.
The transcriptome of partially reprogrammed cells was compared to the transcriptome of the parental fibroblast cells, fully reprogrammed human induced pluripotent stem cells and hESC.
|
| Sample_geo_accession | GSM452352
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 14 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hiPS derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452352/suppl/GSM452352.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452352/suppl/GSM452352.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM452691 | GPL570 |
|
HESC HS181p50
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Human embryonic stem cell line HS181 passage 50
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cell line: HS181, obtained from the Karolinska Institute of Stockholm, Sweden.
cell type: human embryonic stem cells
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The hesc lines hs181 was derived at the Karolinska Institute of Stockholm, Sweden, and cultured on human foreskin fibroblast feeder cells (crl-2429; american type culture collection, manassas, va, http: //www. atcc.org). (Hovatta et al. 2003).
The transcriptome of this hESC was compared to the transcriptome of fully reprogrammed human induced pluripotent stem cells, the parental fibroblast cells and partially reprogrammed cells.
|
| Sample_geo_accession | GSM452691
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 15 2009
| | Sample_last_update_date | Oct 02 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hESCs culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452691/suppl/GSM452691.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452691/suppl/GSM452691.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM452692 | GPL570 |
|
hiPS clone M4C2 p4
|
Induced human pluripotent stem cell clone M4C2 passage 4
|
clone: M4C2
cell type: induced human pluripotent stem cells
|
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Colonies with a full pluripotent morphology were picked up after 35 days, further expanded and characterized.
The transcriptome of this hiPS was compared to the transcriptome of the parental fibroblast cells, partially reprogrammed cells and hESC cells.
|
| Sample_geo_accession | GSM452692
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 15 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hiPS derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452692/suppl/GSM452692.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452692/suppl/GSM452692.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM452693 | GPL570 |
|
hiPS clone M4C10 p4
|
Induced human pluripotent stem cell clone M4C10 passage 4
|
clone: M4C10
cell type: induced human pluripotent stem cells
|
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Colonies with a full pluripotent morphology were picked up after 35 days, further expanded and characterized.
The transcriptome of this hiPS was compared to the transcriptome of the parental fibroblast cells, partially reprogrammed cells and hESC cells.
|
| Sample_geo_accession | GSM452693
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 15 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hiPS derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452693/suppl/GSM452693.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452693/suppl/GSM452693.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM452694 | GPL570 |
|
hiPS clone M5VC2 p4
|
Induced human pluripotent stem cell clone M5VC2 passage 4
|
clone: M5VC2
cell type: induced human pluripotent stem cells
|
Newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Colonies with a full pluripotent morphology were picked up after 35 days, further expanded and characterized.
The transcriptome of this hiPS was compared to the transcriptome of the parental fibroblast cells, partially reprogrammed cells and hESC cells.
|
| Sample_geo_accession | GSM452694
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 15 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for hiPS derivation and culture consisted of 80% KO-DMEM, 20% knockout SR, 2 mM L-glutamine, 1% nonessential amino acids, 0.5 mM β-mercaptoethanol (all from Gibco Invitrogen, Cergy-Pontoise, France) and 10 ng/mL of bFGF (Abcys, Paris, France). All passaging were performed mechanically by cutting colonies using a #15 scalpel under the microscope. Human foreskin fibroblasts (HFF)( SCRC-1041; ATCC, Manassas, VA, USA), mitotically inactivated using irradiation (40 Gy), were used as feeder cells (Hovatta et al. 2003).
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452694/suppl/GSM452694.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM452nnn/GSM452694/suppl/GSM452694.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
| | |
|
GSM453652 | GPL570 |
|
HFF1
|
Human foreskin fibroblasts HFF1
|
cell line: HFF1
cell type: human foreskin fibroblasts
|
For the purpose of a reprogramming experiment, newborn human foreskin fibroblasts were transduced with four lentiviral vectors expressing Oct4, Sox2, Lin28 or Nanog under the control of the human EF1α promoter (Yu et al., 2007, Science vol. 318 pp. 1917-20). Partially and fully reprogrammed hIPS clones were obtained. This sample is the parental foreskin fibroblasts HFF1 cell line.
The transcriptome of this HFF cell sample was compared to the transcriptome of fully and partially reprogrammed cells, and hESC cells.
|
| Sample_geo_accession | GSM453652
| | Sample_status | Public on May 01 2010
| | Sample_submission_date | Sep 17 2009
| | Sample_last_update_date | Sep 24 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | The culture medium used for human foreskin fibroblasts HFF1 cells comprised DMEM Iscove, 10% fetal bovine serum and Pencillin-Streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using RNeasy mini kits (Qiagen) according to the manufacturer's instructions and quantified using a NanoDrop spectrophotometer.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Complementary RNA (cRNA) was prepared according to the manufacturer’s (Affymetrix) protocol ‘small sample protocol II’, starting from 100 ng total RNA.
| | Sample_hyb_protocol | Following fragmentation, cRNA was hybridized for 16 hr at 45C on the GeneChip Human U133 plus 2.0 array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the Affymetrix GeneChip Scanner 3000 7G.
| | Sample_data_processing | Data were analyzed with the GCOS 1.2 software (Affymetrix), using the default analysis settings and global scaling as normalization method, with a trimmed mean target intensity value (TGT) of each array arbitrarily set to 100.
| | Sample_platform_id | GPL570
| | Sample_contact_name | John,,De Vos
| | Sample_contact_email | john.devos@inserm.fr
| | Sample_contact_laboratory | Microarray Core Facility
| | Sample_contact_department | Institute for Research in Biotherapy
| | Sample_contact_institute | University Hospital of Montpellier
| | Sample_contact_address | 80 av. Augustin Fliche
| | Sample_contact_city | Montpellier
| | Sample_contact_zip/postal_code | 34000
| | Sample_contact_country | France
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM453nnn/GSM453652/suppl/GSM453652.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM453nnn/GSM453652/suppl/GSM453652.CHP.gz
| | Sample_series_id | GSE18147
| | Sample_series_id | GSE18265
| | Sample_data_row_count | 54675
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