Search results for the GEO ID: GSE33112  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM820036 | GPL570 |
|
Colo200_TOP_high
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Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: Colo200
cell fraction: high
|
ext096
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820036
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820036/suppl/GSM820036.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820037 | GPL570 |
|
Colo200_TOP_low
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: Colo200
cell fraction: low
|
ext097
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820037
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820037/suppl/GSM820037.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820038 | GPL570 |
|
Colo100_TOP_high
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: Colo200
cell fraction: high
|
ext094
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820038
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820038/suppl/GSM820038.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820039 | GPL570 |
|
Colo100_TOP_low
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: Colo200
cell fraction: low
|
ext095
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820039
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820039/suppl/GSM820039.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820040 | GPL570 |
|
LM003_TOP_low
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: LM003
cell fraction: low
|
ext112
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820040
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820040/suppl/GSM820040.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820041 | GPL570 |
|
LM003_TOP_high
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: LM003
cell fraction: high
|
ext114
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820041
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820041/suppl/GSM820041.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820042 | GPL570 |
|
co108_TOP_ high
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: co108
cell fraction: high
|
ext246
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820042
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820042/suppl/GSM820042.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820043 | GPL570 |
|
co108_TOP_low
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: co108
cell fraction: low
|
ext247
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820043
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820043/suppl/GSM820043.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820044 | GPL570 |
|
lm23_TOP_high
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: lm23
cell fraction: high
|
ext248
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820044
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820044/suppl/GSM820044.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820045 | GPL570 |
|
lm23_TOP_low
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: lm23
cell fraction: low
|
ext249
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820045
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820045/suppl/GSM820045.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820046 | GPL570 |
|
Colo100.1_TOP_low
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Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: Colo100.1
cell fraction: low
|
ext108
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820046
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820046/suppl/GSM820046.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
| | |
|
GSM820047 | GPL570 |
|
Colo100.1_TOP_high
|
Colon cancer stem cell culture
|
tissue: Colon CSC culture transduced with Wnt reporter construct
cell type: Colo100.1
cell fraction: high
|
ext110
Total RNA from cells comprising the lowest and highest 10% TOP–GFP of spheroidal colon CSC cultures was extracted with Trizol reagent (Invitrogen) in accordance with the manufacturer's protocol. RNA concentration was determined with NanoDrop ND-1000, and quality was determined using the RNA 6000 Nano assay on the Agilent 2100 Bioanalyzer (Agilent Technologies). Affymetrix microarray analysis, fragmentation of RNA, labelling, hybridization to Human Genome U133 Plus 2.0 microarrays, and scanning were performed in accordance with the manufacturer's protocol (Affymetrix).
|
| Sample_geo_accession | GSM820047
| | Sample_status | Public on Nov 05 2011
| | Sample_submission_date | Oct 20 2011
| | Sample_last_update_date | Nov 05 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_growth_protocol_ch1 | CSCs were cultured in modified neurobasal A medium containing N2 supplement (Invitrogen), Lipid Mixture-1 (Sigma), basic fibroblast growth factor (bFGF; 20 ng ml−1) and epidermal growth factor (EGF; 50 ng ml−1).
| | 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 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 protoco
| | 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/GSM820nnn/GSM820047/suppl/GSM820047.CEL.gz
| | Sample_series_id | GSE33112
| | Sample_series_id | GSE33114
| | Sample_data_row_count | 54675
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