Search results for the GEO ID: GSE12399  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM311246 | GPL201 |
|
Adipose tissue-derived MSC
|
Human subcutaneous adipose tissue
|
Adipose tissue (AT) was obtained from a patient (male, 52 year old) undergoing partial abdominoplasty.
|
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.
|
| Sample_geo_accession | GSM311246
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | Sep 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | AT was extensively washed in PBS, dissected into small pieces and digested with 0.1% collagenase for 30 minutes at 37°C. Then, the solution was filtered through a 100um mesh filter, and the cell suspension was cultured in DMEM supplemented with 10% FBS and 2ng/ml FGF-beta. Cells were expanded in vitro and harvested at culture passage 4 for this experiment.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. An additional on-column DNase incubation was added, allowing the selective removal of genomic DNA during the isolation procedure. 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 | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| | Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. 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, statistical analysis and functional categorization.
| | 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/GSM311nnn/GSM311246/suppl/GSM311246.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311246/suppl/GSM311246.CHP.gz
| | Sample_series_id | GSE12399
| | Sample_data_row_count | 8793
| | |
|
GSM311247 | GPL201 |
|
Adipose tissue-derived hepatocyte-like cells 1
|
Human subcutaneous adipose tissue
|
Adipose tissue was obtained from a patient (male, 52 year old) undergoing partial abdominolasty
|
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.
|
| Sample_geo_accession | GSM311247
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | Sep 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At passage culture 4, cells were submitted to the in vitro hepatogenic regimen. Briefly, serum was depleted for 48 hours. Cells were cultured for 2 weeks in the induction medium consisting in DMEM supplemented with 2% FBS, 4.9mM nicotinamide, 20ng/ml hepatocyte growth factor, and 10ng/ml fibroblast growth factor beta. Then, cells were cultured for 2 other weeks in maturation medium containing DMEM supplemented with 2% FBS, 4.9mM nicotinamdie and 20ng/ml oncostatin M.
| | Sample_growth_protocol_ch1 | AT was extensively washed in PBS, dissected into small pieces and digested with 0.1% collagenase for 30 minutes at 37°C. Then, the solution was filtered through a 100um mesh filter, and the cell suspension was cultured in DMEM supplemented with 10% FBS and 2ng/ml FGF-beta. Cells were expanded in vitro up to culture passage 4, before initiating the hepatogenic conversion.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. An additional on-column DNase incubation was added, allowing the selective removal of genomic DNA during the isolation procedure. 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 | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| | Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. 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, statistical analysis and functional categorization.
| | 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/GSM311nnn/GSM311247/suppl/GSM311247.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311247/suppl/GSM311247.CHP.gz
| | Sample_series_id | GSE12399
| | Sample_data_row_count | 8793
| | |
|
GSM311248 | GPL201 |
|
Adipose tissue-derived hepatocyte-like cells 2
|
Human subcutaneous adipose tissue
|
Adipose tissue was obtained from a female (42 year old ) patient undergoing partial abdominoplasty.
|
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.
|
| Sample_geo_accession | GSM311248
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | Sep 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | At passage culture 4, cells were submitted to the in vitro hepatogenic regimen. Briefly, serum was depleted for 48 hours. Cells were cultured for 2 weeks in the induction medium consisting in DMEM supplemented with 2% FBS, 4.9mM nicotinamide, 20ng/ml hepatocyte growth factor, and 10ng/ml fibroblast growth factor beta. Then, cells were cultured for 2 other weeks in maturation medium containing DMEM supplemented with 2% FBS, 4.9mM nicotinamdie and 20ng/ml oncostatin M.
| | Sample_growth_protocol_ch1 | AT was extensively washed in PBS, dissected into small pieces and digested with 0.1% collagenase for 30 minutes at 37°C. Then, the solution was filtered through a 100um mesh filter, and the cell suspension was cultured in DMEM supplemented with 10% FBS and 2ng/ml FGF-beta. Cells were expanded in vitro up to culture passage 4, before initiating the hepatogenic conversion.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. An additional on-column DNase incubation was added, allowing the selective removal of genomic DNA during the isolation procedure. 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 | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| | Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. 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, statistical analysis and functional categorization.
| | 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/GSM311nnn/GSM311248/suppl/GSM311248.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311248/suppl/GSM311248.CHP.gz
| | Sample_series_id | GSE12399
| | Sample_data_row_count | 8793
| | |
|
GSM311250 | GPL201 |
|
Adipose tissue-derived MSC 2
|
Human subcutaneous adipose tissue
|
Adipose tissue was retrieved from a female (42 year old) patient
|
Adipose tissue-derived stromal cells (ATSC) hold great promises for the regenerative medicine, due to their in vitro high proliferative capacity and multilineage differentiation potential. In particular, the hepatic differentiation of ATSC has been so far reported in vitro and in vivo. Molecular mechanisms allowing the differentiation of these cells toward another tissue lineage are however poorly understood. The aim of this study is to compare the transcriptome of ATSC cultured under standard procedure and ATSC cultured for 4 weeks under an hepatogenic regimen.
|
| Sample_geo_accession | GSM311250
| | Sample_status | Public on Dec 01 2008
| | Sample_submission_date | Aug 11 2008
| | Sample_last_update_date | Sep 22 2008
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | AT was extensively washed in PBS, dissected into small pieces and digested with 0.1% collagenase for 30 minutes at 37°C. Then, the solution was filtered through a 100um mesh filter, and the cell suspension was cultured in DMEM supplemented with 10% FBS and 2ng/ml FGF-beta. Cells were expanded in vitro and harvested at culture passage 4 for this experiement.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen) according to the manufacturer's instructions. An additional on-column DNase incubation was added, allowing the selective removal of genomic DNA during the isolation procedure. 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 | Arrays were read with the geneChip Affymetrix 3000 7G scanner.
| | Sample_data_processing | Data were generated by using Affymetrix MAS 5.0 software. 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, statistical analysis and functional categorization.
| | 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/GSM311nnn/GSM311250/suppl/GSM311250.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM311nnn/GSM311250/suppl/GSM311250.CHP.gz
| | Sample_series_id | GSE12399
| | Sample_data_row_count | 8793
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
