Search results for the GEO ID: GSE15132  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM378153 | GPL570 |
|
control 24h (EN 1)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 24 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378153
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378153/suppl/GSM378153.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378154 | GPL570 |
|
ribo deficient 24hr (EN 2)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 24 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378154
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378154/suppl/GSM378154.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378155 | GPL570 |
|
control 48hr (EN 3)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 48 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378155
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378155/suppl/GSM378155.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378156 | GPL570 |
|
ribo deficient 48hr (EN 4)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 48 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378156
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378156/suppl/GSM378156.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378157 | GPL570 |
|
control 72hr (EN 5)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 72 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378157
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378157/suppl/GSM378157.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378158 | GPL570 |
|
ribo deficient 72hr (EN 6)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 72 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378158
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378158/suppl/GSM378158.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378159 | GPL570 |
|
control 24h (EN 7-2)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 24 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378159
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378159/suppl/GSM378159.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378160 | GPL570 |
|
ribo deficient 24hr (EN 8-2)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 24 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378160
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378160/suppl/GSM378160.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378161 | GPL570 |
|
control 48hr (EN 9-2)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 48 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378161
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378161/suppl/GSM378161.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378162 | GPL570 |
|
ribo deficient 48hr (EN 10)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 48 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378162
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378162/suppl/GSM378162.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378163 | GPL570 |
|
control 72hr (EN 11)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 72 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378163
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378163/suppl/GSM378163.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378164 | GPL570 |
|
ribo deficient 72hr (EN 12)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 72 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378164
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378164/suppl/GSM378164.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378165 | GPL570 |
|
control 24h (EN 13)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 24 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378165
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378165/suppl/GSM378165.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378166 | GPL570 |
|
ribo deficient 24hr (EN 14)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 24 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378166
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378166/suppl/GSM378166.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378167 | GPL570 |
|
control 48hr (EN 15)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 48 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378167
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378167/suppl/GSM378167.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378168 | GPL570 |
|
ribo deficient 48hr (EN 16)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 48 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378168
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378168/suppl/GSM378168.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378169 | GPL570 |
|
control 72hr (EN 17)
|
Caco-2
|
cell line: Caco-2
|
Untreated cells after 72 hours
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378169
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378169/suppl/GSM378169.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
GSM378170 | GPL570 |
|
ribo deficient 72hr (EN 18)
|
Caco-2
|
cell line: Caco-2
|
Ribo deficient cells after 72 hour treatment
Gene expression data from human colonic epithelial cells.
|
| Sample_geo_accession | GSM378170
| | Sample_status | Public on Mar 06 2009
| | Sample_submission_date | Mar 05 2009
| | Sample_last_update_date | Mar 05 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | Human colon epithelial (Caco-2) cells were cultured in DMEM or riboflavin-free DMEM (Invitrogen) containing 10% foetal calf serum (FCS) (Harlan Sera-Lab), 100 units/ml penicillin and 100 µg/ml streptomycin (Sigma). Dialysed FCS from the same batch was used where indicated. For clonogenic assays, 0.5 × 106 cells were treated as indicated to differing degrees of riboflavin depletion. After treatment, cells were harvested and plated out at 5,000 cells per well. After growth for 7 days, colonies were fixed, stained with methylene blue and counted
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Qiagen Rneasy RNA Extraction Kit was used for RNA extraction according to manufacturers' instructions
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Biotinylation of antisense RNA carried out according to Affymetrix protocol
| | Sample_hyb_protocol | 15µg of cRNA molecules were heat fragmented and applied to the Human Genome U133 plus2 GeneChip in a hybridisation solution according to the Affymetrix protocol. Hybridisation took place overnight in a rotating hybridisation platform at 45°C for 16 hours. Post hybridisation stringency washing was done using the Affymetrix fluidics station again following the protocol outlined in the Affymetrix instructions
| | Sample_scan_protocol | the GeneChips were scanned in the Affymetrix GCS3000 scanner and the resultant image processed using the GCOS software package to prepare the .CEL files
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100
| | Sample_platform_id | GPL570
| | Sample_contact_name | Paul,Roy,Heath
| | Sample_contact_email | p.heath@sheffield.ac.uk
| | Sample_contact_phone | +44 114 2222254
| | Sample_contact_laboratory | Heath
| | Sample_contact_department | Academic Neurology Unit
| | Sample_contact_institute | University of Sheffield
| | Sample_contact_address | SITraN, 385a Glossop Road
| | Sample_contact_city | Sheffield
| | Sample_contact_state | S. Yorks
| | Sample_contact_zip/postal_code | S10 2HQ
| | Sample_contact_country | United Kingdom
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM378nnn/GSM378170/suppl/GSM378170.CEL.gz
| | Sample_series_id | GSE15132
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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