Search results for the GEO ID: GSE18560  |
(Click on the check boxes provided under "Select for analysis", to initiate grouping) |
(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down) |
|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM461942 | GPL570 |
|
Ls174T-pTER-β-catenin con1
|
Ls174T, β-catenin siRNA, uninduced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: none
time: 72hr
|
Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461942
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461942/suppl/GSM461942.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461943 | GPL570 |
|
Ls174T-L8 dox2
|
Ls174T, dominant-negative Tcf4, induced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: dominant-negative Tcf4 transgene
time: 24hr
|
Ls174T-L8 cells carry a doxycyclin-inducible dominant-negative Tcf4 transgene. Cells were untreated (con) or trangene expression was induced for 24 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461943
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461943/suppl/GSM461943.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461944 | GPL570 |
|
Ls174T-L8 con3
|
Ls174T, dominant-negative Tcf4, uninduced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: none
time: 24hr
|
Ls174T-L8 cells carry a doxycyclin-inducible dominant-negative Tcf4 transgene. Cells were untreated (con) or trangene expression was induced for 24 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461944
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461944/suppl/GSM461944.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461945 | GPL570 |
|
Ls174T-L8 dox3
|
Ls174T, dominant-negative Tcf4, induced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: dominant-negative Tcf4 transgene
time: 24hr
|
Ls174T-L8 cells carry a doxycyclin-inducible dominant-negative Tcf4 transgene. Cells were untreated (con) or trangene expression was induced for 24 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461945
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461945/suppl/GSM461945.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461946 | GPL570 |
|
Ls174T-pTER-β-catenin dox1
|
Ls174T, β-catenin siRNA, induced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: shRNA against β-catenin
time: 72hr
|
Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461946
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461946/suppl/GSM461946.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461947 | GPL570 |
|
Ls174T-pTER-β-catenin con2
|
Ls174T, β-catenin siRNA, uninduced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: none
time: 72hr
|
Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461947
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461947/suppl/GSM461947.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461948 | GPL570 |
|
Ls174T-pTER-β-catenin dox2
|
Ls174T, β-catenin siRNA, induced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: shRNA against β-catenin
time: 72hr
|
Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461948
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461948/suppl/GSM461948.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461949 | GPL570 |
|
Ls174T-pTER-β-catenin con3
|
Ls174T, β-catenin siRNA, uninduced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: none
time: 72hr
|
Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461949
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461949/suppl/GSM461949.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461950 | GPL570 |
|
Ls174T-pTER-β-catenin dox3
|
Ls174T, β-catenin siRNA, induced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: shRNA against β-catenin
time: 72hr
|
Ls174T-pTER-β-catenin cells carry a doxycyclin-inducible shRNA against β-catenin. Cells were left untreated (con) or shRNA was induced for 72 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461950
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461950/suppl/GSM461950.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461951 | GPL570 |
|
Ls174T-L8 con1
|
Ls174T, dominant-negative Tcf4, uninduced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: none
time: 24hr
|
Ls174T-L8 cells carry a doxycyclin-inducible dominant-negative Tcf4 transgene. Cells were untreated (con) or trangene expression was induced for 24 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461951
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461951/suppl/GSM461951.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461952 | GPL570 |
|
Ls174T-L8 dox1
|
Ls174T, dominant-negative Tcf4, induced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: dominant-negative Tcf4 transgene
time: 24hr
|
Ls174T-L8 cells carry a doxycyclin-inducible dominant-negative Tcf4 transgene. Cells were untreated (con) or trangene expression was induced for 24 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461952
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461952/suppl/GSM461952.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
GSM461953 | GPL570 |
|
Ls174T-L8 con2
|
Ls174T, dominant-negative Tcf4, uninduced
|
cell line: Ls174T
cell type: intestinal colorectal carcinoma cells
induction: none
time: 24hr
|
Ls174T-L8 cells carry a doxycyclin-inducible dominant-negative Tcf4 transgene. Cells were untreated (con) or trangene expression was induced for 24 hours with doxycycline (dox). Total RNA was isolated and analyzed on Affymetrix U133 Plus 2.0 to generate expression profiles.
|
| Sample_geo_accession | GSM461953
| | Sample_status | Public on Nov 29 2011
| | Sample_submission_date | Oct 14 2009
| | Sample_last_update_date | Nov 29 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were grown in the presence or absence of doxycycline for 24 hours for Ls174T-L8 or 72 hours for Ls174T-pTER-β-catenin cells.
| | Sample_growth_protocol_ch1 | Appr. 10 million cells were cultured in RPMI (Invitrogen) containing 5% fetal calf serum at 37 degrees Celsius.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was isolated using Trizol (Invitrogen) and purified with RNeasy (Qiagen) according to manufacturer’s protocol.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | RNA sample integrity was checked on an Agilent 2100 Bioanalyzer (Agilent Technologies). 4 µg of total RNA was used for cRNA synthesis and fragmented. Labeling was performed with One-Cycle cDNA synthesis Kit (Affymetrix) according to manufacturer’s protocol. Sample quality was checked on a Bioanalyzer prior and after fragmentation.
| | Sample_hyb_protocol | 10 µg of labeled cRNA was hybridized to the Affymetrix Human Genome U133 Plus 2.0 arrays according to manufacturer’s protocol (Affymetrix).
| | Sample_scan_protocol | Arrays were scanned with a GeneChip Scanner 3000 (Affymetrix) according to manufacturer’s protocol.
| | Sample_data_processing = Expression data (cel files) were normalized with the MAS5.0 algorithm (target signal | 100) using GCOS software (Affymetrix).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Rogier,,Versteeg
| | Sample_contact_email | r.versteeg@amc.uva.nl
| | Sample_contact_department | Department of Human Genetics
| | Sample_contact_institute | Academic Medical Centre, University of Amsterdam
| | Sample_contact_address | P.O. Box 22700
| | Sample_contact_city | Amsterdam
| | Sample_contact_zip/postal_code | 1100DE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM461nnn/GSM461953/suppl/GSM461953.CEL.gz
| | Sample_series_id | GSE18560
| | Sample_data_row_count | 54675
| | |
|
| |
| |
Make groups for comparisons |
(2 groups will be compared at a time) |
|
| Select GSMs and click on "Add groups" |
Enter the group name here: |
|
|
|
