Search results for the GEO ID: GSE22865  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM564950 | GPL570 |
|
Hs578T set 1 CDH13 M
|
Hs578T, methylated CDH13 sequence (CDH13 M)
|
cell line: Hs578T
cell type: breast cancer
treatment: CDH13 M
|
Gene expression data of the human breast cancer cell line Hs578T treated with a methylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 M).
Biological replicate.
0415_016_Hs578T-M_h01_SJ_130406
|
| Sample_geo_accession | GSM564950
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564950/suppl/GSM564950.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564951 | GPL570 |
|
Hs578T set 1 CDH13 U
|
Hs578T, unmethylated CDH13 sequence (CDH13 U)
|
cell line: Hs578T
cell type: breast cancer
treatment: CDH13 U
|
Gene expression data of the human breast cancer cell line Hs578T treated with unmethylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 U).
Biological replicate.
0416_016_Hs578T-U_h01_SJ_130406
|
| Sample_geo_accession | GSM564951
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564951/suppl/GSM564951.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564952 | GPL570 |
|
BT-20 set 1 CDH13 M
|
BT-20, methylated CDH13 sequence (CDH13 M)
|
cell line: BT-20
cell type: breast cancer
treatment: CDH13 M
|
Gene expression data of the human breast cancer cell line BT-20 treated with a methylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 M).
Biological replicate.
0417_016_BT20-M_h01_SJ_130406
|
| Sample_geo_accession | GSM564952
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564952/suppl/GSM564952.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564953 | GPL570 |
|
BT-20 set 1 CDH13 U
|
BT-20, unmethylated CDH13 sequence (CDH13 U)
|
cell line: BT-20
cell type: breast cancer
treatment: CDH13 U
|
Gene expression data of the human breast cancer cell line BT-20 treated with unmethylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 U).
Biological replicate.
0418_016_BT20-U_h01_SJ_130406
|
| Sample_geo_accession | GSM564953
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564953/suppl/GSM564953.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564954 | GPL570 |
|
Hs578T set 2 CDH13 M
|
Hs578T, methylated CDH13 sequence (CDH13 M)
|
cell line: Hs578T
cell type: breast cancer
treatment: CDH13 M
|
Gene expression data of the human breast cancer cell line Hs578T treated with a methylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 M).
Biological replicate.
0462_016_Hs578T-M_h01_SJ_240506
|
| Sample_geo_accession | GSM564954
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564954/suppl/GSM564954.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564955 | GPL570 |
|
Hs578T set 2 CDH13 U
|
Hs578T, unmethylated CDH13 sequence (CDH13 U)
|
cell line: Hs578T
cell type: breast cancer
treatment: CDH13 U
|
Gene expression data of the human breast cancer cell line Hs578T treated with unmethylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 U).
Biological replicate.
0463_016_Hs578T-U_h01_SJ_240506
|
| Sample_geo_accession | GSM564955
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564955/suppl/GSM564955.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564956 | GPL570 |
|
Hs578T CDH13 ODN
|
Hs578T, ODN 2006
|
cell line: Hs578T
cell type: breast cancer
treatment: ODN 2006
|
Gene expression data of the human breast cancer cell line Hs578T treated with ODN 2006.
0464_016_HsODN_h01_SJ_240506
|
| Sample_geo_accession | GSM564956
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564956/suppl/GSM564956.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564957 | GPL570 |
|
Hs578T CDH13 ODN CTL
|
Hs578T, ODN 2006 CTL
|
cell line: Hs578T
cell type: breast cancer
treatment: ODN 2006 CTL
|
Gene expression data of the human breast cancer cell line Hs578T treated with ODN 2006 CTL.
0465_016_HsODN-CT_h01_SJ_240506
|
| Sample_geo_accession | GSM564957
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564957/suppl/GSM564957.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564958 | GPL570 |
|
BT-20 set 2 CDH13 M
|
BT-20, methylated CDH13 sequence (CDH13 M)
|
cell line: BT-20
cell type: breast cancer
treatment: CDH13 M
|
Gene expression data of the human breast cancer cell line BT-20 treated with a methylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 M).
Biological replicate.
0466_016_BT-20-M_h01_SJ_240506
|
| Sample_geo_accession | GSM564958
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564958/suppl/GSM564958.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564959 | GPL570 |
|
BT-20 set 2 CDH13 U
|
BT-20, unmethylated CDH13 sequence (CDH13 U)
|
cell line: BT-20
cell type: breast cancer
treatment: CDH13 U
|
Gene expression data of the human breast cancer cell line BT-20 treated with unmethylated DNA sequence with 4 CpG motifs from exon 1 region of CDH13 (CDH13 U).
Biological replicate.
0467_016_BT-20-U_h01_SJ_240506
|
| Sample_geo_accession | GSM564959
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564959/suppl/GSM564959.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564960 | GPL570 |
|
BT-20 CDH13 ODN
|
BT-20, ODN 2006
|
cell line: BT-20
cell type: breast cancer
treatment: ODN 2006
|
Gene expression data of the human breast cancer cell line BT-20 treated with ODN 2006.
0468_016_BT20ODN_h01_SJ_240506
|
| Sample_geo_accession | GSM564960
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564960/suppl/GSM564960.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
GSM564961 | GPL570 |
|
BT-20 CDH13 ODN CTL
|
BT-20, ODN 2006 CTL
|
cell line: BT-20
cell type: breast cancer
treatment: ODN 2006 CTL
|
Gene expression data of the human breast cancer cell line BT-20 treated with ODN 2006 CTL.
0469_016_BTODN-CT_h01_SJ_240506
|
| Sample_geo_accession | GSM564961
| | Sample_status | Public on Dec 01 2011
| | Sample_submission_date | Jul 09 2010
| | Sample_last_update_date | Dec 02 2011
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | BT-20 and Hs578T breast cancer cells were treated with different CpG-containing oligonucleotides.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | In more detail:
| | Sample_treatment_protocol_ch1 | Cells were treated with a 200 nM final concentration of different oligonucleotides:
| | Sample_treatment_protocol_ch1 | CpG-DNA (ODN2006, InvivoGen, San Diego, California, USA; 5'-TCGTCGTTTTGTCGTTTTGTCGTT-3'),
| | Sample_treatment_protocol_ch1 | GpC-DNA (ODN2006 CTR, InvivoGen, San Diego, California, USA; 5'-TGCTGCTTTTGTGCTTTTGTGCTT-3'),
| | Sample_treatment_protocol_ch1 | CDH13 U (5'-TCGGATCGCCCGGCACGGGCAGGGTGAGGG-3', CDH13 U complementary strand: 5'-CCCTCACCCTGCCCGTGCCGGGCGATCCGA-3'), and
| | Sample_treatment_protocol_ch1 | CDH13 M (sequence is identical to dsCDH13 U, but the cytosines at positions 2, 7, 11, and 16 and at positions 14, 19, 23, and 28 in the complementary strand are methylated)
| | Sample_treatment_protocol_ch1 | with 3µg DOTAP Liposomal Transfection Reagent per µg DNA (Roche Diagnostics, Mannheim, Germany) for 24 hours. Transfection agent and ODNs handling was according to the manufacturer's working instructions. After treatment, cells were harvested using Accutase (PAA Laboratories GmbH, Pasching, Austria), washed with PBS and frozen at -80°C.
| | Sample_growth_protocol_ch1 | Human breast cancer cell lines BT-20 and Hs578T were obtained from the American Type Culture Collection (ATCC) in 2001 or 2006, respectively. Cells were cultured in large cell culture flasks in MEM Medium with Earle’s Salts (Gibco # 21090-022), 10% FCS, and 2 mM L-Glutamine at 37°C and 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Tri Reagent (Molecular Research Center, Inc.) extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | 1ug total RNA was processed to generate a biotinylated hybridization target using “One Cycle cDNA Synthesis” and “One Cycle Target Labelling” kits from Affymetrix (Affymetrix, Santa Clara, CA). All procedures were performed according to the manufacturer’s protocols.
| | Sample_hyb_protocol | 20ug of cRNA were fragmented at 95C using the Affymetrix fragmentation buffer, mixed with hybridization buffer containing hybridization controls and hybridized to Affymetrix HG U133 Plus 2.0 GeneChips.
| | Sample_scan_protocol | Fluorescence signals were recorded by an Affymetrix scanner 3000 and image analysis was performed with the GCOS software.
| | Sample_data_processing | The raw signal intensities were preprocessed in R (version 2.4) using the GCRMA algorithm (Bioconductor version 1.9).
| | Sample_platform_id | GPL570
| | Sample_contact_name | Johannes,,Rainer
| | Sample_contact_email | johannes.rainer@i-med.ac.at
| | Sample_contact_laboratory | Applied Bioinformatics Group
| | Sample_contact_department | Biocenter, Division Molecular Pathophysiology
| | Sample_contact_institute | Medical University Innsbruck
| | Sample_contact_address | Innrain 80-82 II
| | Sample_contact_city | Innsbruck
| | Sample_contact_zip/postal_code | 6020
| | Sample_contact_country | Austria
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM564nnn/GSM564961/suppl/GSM564961.CEL.gz
| | Sample_series_id | GSE22865
| | Sample_data_row_count | 54675
| | |
|
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