Result

Search results for the GEO ID: GSE18201

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GPL ID

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Title

Source name

Description

Characteristics

GSM455150

GPL201

Adipose tissue-derived MSC (patient 1)

Human subcutaneous adipose tissue

cell type: Adipose tissue-derived mesenchymal-stromal cell

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	GSM455150
Sample_status	Public on Dec 15 2009
Sample_submission_date	Sep 22 2009
Sample_last_update_date	Sep 23 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Adipose tissue 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.
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 GCOS v1.2 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.
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/GSM455nnn/GSM455150/suppl/GSM455150_ctrl_P1.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455150/suppl/GSM455150_ctrl_P1.CHP.gz
Sample_series_id	GSE18201
Sample_data_row_count	8793

GSM455151

GPL201

Adipose tissue-derived MSC (patient 2)

Human subcutaneous adipose tissue

cell type: Adipose tissue-derived mesenchymal-stromal cell

Adipose tissue was retrieved from a male (49 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	GSM455151
Sample_status	Public on Dec 15 2009
Sample_submission_date	Sep 22 2009
Sample_last_update_date	Sep 23 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Adipose tissue 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.
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 GCOS v1.2 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.
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/GSM455nnn/GSM455151/suppl/GSM455151_ctrl_P5.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455151/suppl/GSM455151_ctrl_P5.CHP.gz
Sample_series_id	GSE18201
Sample_data_row_count	8793

GSM455152

GPL201

Adipose tissue-derived MSC (patient 3)

Human subcutaneous adipose tissue

cell type: Adipose tissue-derived mesenchymal-stromal cell

Adipose tissue was retrieved from a female (51 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	GSM455152
Sample_status	Public on Dec 15 2009
Sample_submission_date	Sep 22 2009
Sample_last_update_date	Sep 23 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	Adipose tissue 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.
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 GCOS v1.2 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.
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/GSM455nnn/GSM455152/suppl/GSM455152_ctrl_P7.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455152/suppl/GSM455152_ctrl_P7.CHP.gz
Sample_series_id	GSE18201
Sample_data_row_count	8793

GSM455153

GPL201

ATSC differentiated toward the hepatic lineage (patient 1)

Human subcutaneous adipose tissue

cell type: Adipose tissue-derived stromal cell differentiated toward the hepatic lineage

Sample_geo_accession	GSM455153
Sample_status	Public on Dec 15 2009
Sample_submission_date	Sep 22 2009
Sample_last_update_date	Sep 23 2009
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	Adipose tissue 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.
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 GCOS v1.2 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.
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/GSM455nnn/GSM455153/suppl/GSM455153_diff_P2.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455153/suppl/GSM455153_diff_P2.CHP.gz
Sample_series_id	GSE18201
Sample_data_row_count	8793

GSM455154

GPL201

ATSC differentiated toward the hepatic lineage (patient 2)

Human subcutaneous adipose tissue

cell type: Adipose tissue-derived stromal cell differentiated toward the hepatic lineage

Adipose tissue was obtained from a male (49 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	GSM455154
Sample_status	Public on Dec 15 2009
Sample_submission_date	Sep 22 2009
Sample_last_update_date	Sep 23 2009
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	Adipose tissue 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.
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 GCOS v1.2 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.
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/GSM455nnn/GSM455154/suppl/GSM455154_diff_P6.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455154/suppl/GSM455154_diff_P6.CHP.gz
Sample_series_id	GSE18201
Sample_data_row_count	8793

GSM455155

GPL201

ATSC differentiated toward the hepatic lineage (patient 3)

Human subcutaneous adipose tissue

cell type: Adipose tissue-derived stromal cell differentiated toward the hepatic lineage

Adipose tissue was obtained from a male (51 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	GSM455155
Sample_status	Public on Dec 15 2009
Sample_submission_date	Sep 22 2009
Sample_last_update_date	Sep 23 2009
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	Adipose tissue 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.
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 GCOS v1.2 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.
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/GSM455nnn/GSM455155/suppl/GSM455155_diff_P3.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM455nnn/GSM455155/suppl/GSM455155_diff_P3.CHP.gz
Sample_series_id	GSE18201
Sample_data_row_count	8793

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