Search results for the GEO ID: GSE8954  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM226880 | GPL201 |
|
Adipose tissue derived MSC_patient 1
|
human sub-cutaneous adipose tissue
|
Cultivated mesenchymal stem cells (P4) isolated from adipose tissue. Adipose tissue specimens were acquired from exceeding tissues removed during partial abdominoplasty.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226880
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of cultivated adipose tissue-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226880/suppl/GSM226880.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226880/suppl/GSM226880.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226881 | GPL201 |
|
Adipose tissue derived-MSC_patient 2
|
sub-cutaneous adipose tissue
|
Cultivated mesenchymal stem cells (passage ) isolated from human adipose tissue extracted from a patient during surgical procedures.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226881
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of cultivated adipose tissue-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226881/suppl/GSM226881.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226881/suppl/GSM226881.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226882 | GPL201 |
|
Adipose tissue derived-MSC_patient 3
|
sub-cutaneous human adipose tissue
|
Cultivated mesenchymal stem cells (passage4) isolated from human adipose tissue extracted from a patient during surgical procedures.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226882
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of cultivated adipose tissue-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226882/suppl/GSM226882.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226882/suppl/GSM226882.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226883 | GPL201 |
|
Adipose tissue derived-MSC_patient 4
|
human sub-cutaneous adipose tissue
|
Cultivated mesenchymal stem cells (passage4) isolated from human adipose tissue extracted from a patient during surgical procedures.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226883
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of cultivated adipose tissue-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226883/suppl/GSM226883.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226883/suppl/GSM226883.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226884 | GPL201 |
|
Bone marrow derived-MSC_patient 1
|
Human bone marrow
|
1.077g/cm3) and resuspended in Mesenchymal Stem Cell Medium (MSCGM) to allow the selection of mesenchymal stem cells via their property of adherence to the plastic.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226884
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of cultivated bone marrow-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226884/suppl/GSM226884.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226884/suppl/GSM226884.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226885 | GPL201 |
|
Bone marrow derived-MSC_patient 2
|
human bone marrow
|
1.077g/cm3) and resuspended in Mesenchymal Stem Cell Medium (MSCGM) to allow the selection of mesenchymal stem cells via their property of adherence to the plastic.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226885
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of cultivated bone marrow-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226885/suppl/GSM226885.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226885/suppl/GSM226885.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226886 | GPL201 |
|
Bone marrow derived-MSC_patient 3
|
human bone marrow
|
1.077g/cm3) and resuspended in Mesenchymal Stem Cell Medium (MSCGM) to allow the selection of mesenchymal stem cells via their property of adherence to the plastic.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226886
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of cultivated bone marrow-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226886/suppl/GSM226886.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226886/suppl/GSM226886.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226887 | GPL201 |
|
Bone marrow derived-MSC_patient 4
|
human bone marrow
|
1.077g/cm3) and resuspended in Mesenchymal Stem Cell Medium (MSCGM) to allow the selection of mesenchymal stem cells via their property of adherence to the plastic.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226887
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in Mesenchymal Stem Cell medium (MSCGM) (Cambrex Inc.)
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of cultivated bone marrow-derived mesenchymal stem cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226887/suppl/GSM226887.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226887/suppl/GSM226887.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226888 | GPL201 |
|
MRC-5 cells_replicate 1
|
MRC-5 cell line (diploid human embryonic lung fibroblasts)
|
Since Mesenchymal stem cells (MSC) are direct precursors of fibroblasts, we assumed that MRC-5 fibroblasts exhibit a large degree of similarity with MSC. Thus, by using MRC-5 cells as control in our study, we expected to rule out a large number of genes regulating cell homeostasis and select genes related to stemness.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226888
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM additioned with 10% fetal bovine serum (FBS) and 1% of antibiotics.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of MRC-5 cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226888/suppl/GSM226888.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226888/suppl/GSM226888.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226889 | GPL201 |
|
MRC-5 cells_replicate 2
|
MRC-5 cell line (diploid human embryonic lung fibroblasts)
|
Since Mesenchymal stem cells (MSC) are direct precursors of fibroblasts, we assumed that MRC-5 fibroblasts exhibit a large degree of similarity with MSC. Thus, by using MRC-5 cells as control in our study, we expected to rule out a large number of genes regulating cell homeostasis and select genes related to stemness.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226889
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM additioned with 10% fetal bovine serum (FBS) and 1% of antibiotics.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of MRC-5 cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226889/suppl/GSM226889.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226889/suppl/GSM226889.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
|
GSM226890 | GPL201 |
|
MRC-5 cells_replicate 3
|
MRC-5 cell line (diploid human embryonic lung fibroblasts)
|
Since Mesenchymal stem cells (MSC) are direct precursors of fibroblasts, we assumed that MRC-5 fibroblasts exhibit a large degree of similarity with MSC. Thus, by using MRC-5 cells as control in our study, we expected to rule out a large number of genes regulating cell homeostasis and select genes related to stemness.
|
Bone marrow (BM) has been considered so far the reference source for stromal cells (SC) originally called mesenchymal stem cells. Recently human adult adipose tissue (AT) has been reported as a valuable source for the isolation of cells exerting a mesenchymal-like phenotype. Though both BM- and AT- derived stromal cells (BMSC and ATSC) share similar immuno-phenotype and exhibit multi-lineage potential in vitro, a consensual panel of specific markers is still debated and the precise molecular mechanisms governing their differentiated fate are not fully understood.
The aim of this study was to compare the genome wide expression profiles of stromal cells isolated from AT and BM and to emphasize the core of MSC stemness properties. Moreover we focused on the molecular characteristics of ATSC, attempting to reveal their specific features.
|
| Sample_geo_accession | GSM226890
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Sep 05 2007
| | Sample_last_update_date | Aug 14 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Cells were grown in DMEM additioned with 10% fetal bovine serum (FBS) and 1% of antibiotics.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA from 1 million of MRC-5 cells was isolated using the RNeasy Plus mini kit (Qiagen) according to the manufacturer's instructions. This kit allows the selective retrieval of RNA and the removal of double-stranded DNA during the extraction process. RNA was quantified by UV spectrophotometer and quality was assessed on agarose gel.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Labeling protocol was accomplished according to Affymetrix recommended protocol. Briefly, following cDNA synthesis, the material was amplified and labeled with biotinylated dNTPs during an in vitro transcription (IVT) using the GeneChip Expression 3' Amplification One-Cycle target Labeling and Control Reagents (Affymetrix Inc.)
| | Sample_hyb_protocol | Biotin-labeled cRNA was purified and chemically fragmented according to Affymetrix's protocol. Ten micrograms of fragmented and biotin-labeled cRNA were hybridized onto Human Focus array at 45°C for 16 hours in a rotisserie oven set at 60RPM. The following day, the chip was washed and labeled with streptavidin-phycoerythrin in a fluidic station using the EukGE-WS2v5 protocol according to Affymetrix' s recommendation.
| | Sample_scan_protocol | GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
| | Sample_data_processing | The data were generated by using Affymetrix MAS 5.0 softwware. Briefly, the signal value was calculated from the combined background-adjusted, PerfectMatch and MisMatch values of the probe set using predefined algorithms of MAS 5.0 software. Data set was further exported to Genespring software for normalization and statistical analysis.
| | Sample_platform_id | GPL201
| | Sample_contact_name | Nathalie,,Saulnier
| | Sample_contact_email | nathalie.saulnier@rm.unicatt.it
| | Sample_contact_phone | +39 0630154915
| | Sample_contact_fax | +39 0630154813
| | Sample_contact_institute | Università Cattolica del Sacro Cuore di Roma
| | Sample_contact_address | Largo Francesco Vito,1
| | Sample_contact_city | Roma
| | Sample_contact_zip/postal_code | 00168
| | Sample_contact_country | Italy
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226890/suppl/GSM226890.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM226nnn/GSM226890/suppl/GSM226890.CHP.gz
| | Sample_series_id | GSE8954
| | Sample_data_row_count | 8793
| | |
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