Search results for the GEO ID: GSE28792  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM713153 | GPL570 |
|
Medium-only
|
medium treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713153
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713153/suppl/GSM713153.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713154 | GPL570 |
|
100 mM NaCl
|
100 mM NaCl treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713154
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713154/suppl/GSM713154.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713155 | GPL570 |
|
5 mM butyrate
|
5 mM butyrate treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713155
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713155/suppl/GSM713155.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713156 | GPL570 |
|
0% polydextrose vessel 1
|
0% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713156
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713156/suppl/GSM713156.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713157 | GPL570 |
|
0% polydextrose vessel 2
|
0% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713157
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713157/suppl/GSM713157.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713158 | GPL570 |
|
0% polydextrose vessel 3
|
0% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713158
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713158/suppl/GSM713158.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713159 | GPL570 |
|
0% polydextrose vessel 4
|
0% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713159
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713159/suppl/GSM713159.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713160 | GPL570 |
|
1% polydextrose vessel 1
|
1% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713160
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713160/suppl/GSM713160.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713161 | GPL570 |
|
1% polydextrose vessel 2
|
1% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713161
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713161/suppl/GSM713161.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713162 | GPL570 |
|
1% polydextrose vessel 3
|
1% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713162
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713162/suppl/GSM713162.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713163 | GPL570 |
|
1% polydextrose vessel 4
|
1% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713163
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713163/suppl/GSM713163.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713164 | GPL570 |
|
2% polydextrose vessel 1
|
2% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713164
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713164/suppl/GSM713164.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713165 | GPL570 |
|
2% polydextrose vessel 2
|
2% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713165
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713165/suppl/GSM713165.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713166 | GPL570 |
|
2% polydextrose vessel 3
|
2% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713166
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713166/suppl/GSM713166.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
GSM713167 | GPL570 |
|
2% polydextrose vessel 4
|
2% PDX fermentation metabolite-treated, 24h
|
cell line: non-differentiated Caco-2 intestinal epithelial cell line
|
|
| Sample_geo_accession | GSM713167
| | Sample_status | Public on Apr 22 2011
| | Sample_submission_date | Apr 21 2011
| | Sample_last_update_date | Apr 28 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Polydextrose was fermented with semi-continuous colon silmulator in which a single unit consists of four sequentially connected glass vessels, V1 to V4, in which the conditions are adjusted to represent the different compartments of the colon, V1 representing ascending colon, V2 transverse colon, V3 descending colon, and V4 sigmoid/rectum area. The simulation was performed for 48 hours as in Makivuokko H, Nurmi J, Nurminen P, Stowell J, Rautonen N (2005) In vitro effects on polydextrose by colonic bacteria and caco-2 cell cyclooxygenase gene expression. Nutr Cancer 52 (1):94-104. Non-differentiated Caco-2 cells were treated with 5mM butyrate, 100 mM NaCl and 10 % (vol/vol) containing 0%, 1% and 2% polydextrose fermentation metabolites from which bacterial cells and other debris was removed by centifugation (10 000 × g, 5 minutes)diluted in serum-free DMEM for 24 hours.
| | Sample_growth_protocol_ch1 | Caco-2 cells were maintained in Dulbecco's modified Eagle's medium supplemented with non-essential amino acids (Invitrogen, Carlsbad, CA, US), 1 mM sodium Puryvate (Invitrogen), and 20 Uml-1 penicillin (Invitrogen), 20 µgml-1 streptomycin (Invitrogen), 0.5 µgml-1 amphotericin (Invitrogen), and 5 % fetal bovine serum (Invitrogen) at +37 °C in 5 % air atmosphere.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to manufacturer’ s instructions. DNase treatment was included to remove the residual DNA contamination.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix standard protocol
| | Sample_hyb_protocol | Affymetrix standard protocol; after fragmentation, 15 ug of cRNA was hybridized for 16 hours at 45 C on Affymetrix U133 plus 2.0 arrays. GeneChips were washed and stained in Affymetrix Fluidics Station.
| | Sample_scan_protocol | Affymetrix standard protocol using type M10 scanner
| | Sample_data_processing | The analysis was performed using R/Bioconductor, and the data was normalized using GC-RMA algorithm.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Esa,,Alhoniemi
| | Sample_contact_institute | Pharmatest Services Ltd
| | Sample_contact_address | Itäinen Pitkäkatu 4 C
| | Sample_contact_city | Turku
| | Sample_contact_zip/postal_code | FI-20520
| | Sample_contact_country | Finland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM713nnn/GSM713167/suppl/GSM713167.CEL.gz
| | Sample_series_id | GSE28792
| | Sample_data_row_count | 54675
| | |
|
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