Search results for the GEO ID: GSE28645  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM709764 | GPL570 |
|
LY2 control-siRNA tamoxifen treated rep2
|
LY2 cell line, SRC-1 scrambled treated 120min, biological rep2
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 scrambled
treatment: tamoxifen for 120 min
|
Gene expression data from endocrine resistant breast cancer cell line LY2
|
| Sample_geo_accession | GSM709764
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709764/suppl/GSM709764_S0401F001.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709765 | GPL570 |
|
LY2 SRC1-siRNA untreated rep3
|
LY2 cell line, SRC-1 siRNA untreated, biological rep3
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 siRNA
treatment: untreated
|
Gene expression data from endocrine resistant breast cancer cell line LY3
|
| Sample_geo_accession | GSM709765
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709765/suppl/GSM709765_S0401F002.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709766 | GPL570 |
|
LY2 control-siRNA tamoxifen treated rep3
|
LY2 cell line, SRC-1 scrambled treated 120min, biological rep3
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 scrambled
treatment: tamoxifen for 120 min
|
Gene expression data from endocrine resistant breast cancer cell line LY4
|
| Sample_geo_accession | GSM709766
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709766/suppl/GSM709766_S0401F003.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709767 | GPL570 |
|
LY2 SRC1-siRNA tamoxifen treated rep1
|
LY2 cell line, SRC-1 siRNA treated 120mins, biological rep1
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 siRNA
treatment: tamoxifen for 120 mins
|
Gene expression data from endocrine resistant breast cancer cell line LY5
|
| Sample_geo_accession | GSM709767
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709767/suppl/GSM709767_S0401F004.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709768 | GPL570 |
|
LY2 control-siRNA tamoxifen treated rep1
|
LY2 cell line, SRC-1 scrambled treated 120min, biological rep1
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 scrambled
treatment: tamoxifen for 120 min
|
Gene expression data from endocrine resistant breast cancer cell line LY6
|
| Sample_geo_accession | GSM709768
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709768/suppl/GSM709768_S0401F005.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709769 | GPL570 |
|
LY2 SRC1-siRNA tamoxifen treated rep3
|
LY2 cell line, SRC-1 siRNA treated 120min, biological rep3
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 siRNA
treatment: tamoxifen for 120 min
|
Gene expression data from endocrine resistant breast cancer cell line LY7
|
| Sample_geo_accession | GSM709769
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709769/suppl/GSM709769_S0401F006.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709770 | GPL570 |
|
LY2 control-siRNA untreated rep3
|
LY2 cell line, SRC-1 scrambled untreated, biological rep3
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 scrambled
treatment: untreated
|
Gene expression data from endocrine resistant breast cancer cell line LY8
|
| Sample_geo_accession | GSM709770
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709770/suppl/GSM709770_S0401F007.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709771 | GPL570 |
|
LY2 SRC1-siRNA untreated rep1
|
LY2 cell line, SRC-1 siRNA untreated, biological rep1
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 siRNA
treatment: untreated
|
Gene expression data from endocrine resistant breast cancer cell line LY9
|
| Sample_geo_accession | GSM709771
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709771/suppl/GSM709771_S0401F008.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709772 | GPL570 |
|
LY2 SRC1-siRNA untreated rep2
|
LY2 cell line, SRC-1 siRNA untreated, biological rep2
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 siRNA
treatment: untreated
|
Gene expression data from endocrine resistant breast cancer cell line LY10
|
| Sample_geo_accession | GSM709772
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709772/suppl/GSM709772_S0401F009.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709773 | GPL570 |
|
LY2 control-siRNA untreated rep1
|
LY2 cell line, SRC-1 scrambled untreated, biological rep1
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 scrambled
treatment: untreated
|
Gene expression data from endocrine resistant breast cancer cell line LY11
|
| Sample_geo_accession | GSM709773
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709773/suppl/GSM709773_S0401F010.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709774 | GPL570 |
|
LY2 control-siRNA untreated rep2
|
LY2 cell line, SRC-1 scrambled untreated, biological rep2
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 scrambled
treatment: untreated
|
Gene expression data from endocrine resistant breast cancer cell line LY12
|
| Sample_geo_accession | GSM709774
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709774/suppl/GSM709774_S0401F011.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709775 | GPL570 |
|
LY2 SRC1-siRNA untreated rep4
|
LY2 cell line, SRC-1 siRNA untreated, biological rep4
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 siRNA
treatment: untreated
|
Gene expression data from endocrine resistant breast cancer cell line LY13
|
| Sample_geo_accession | GSM709775
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709775/suppl/GSM709775_S0401F013.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709776 | GPL570 |
|
LY2 control-siRNA untreated rep4
|
LY2 cell line, SRC-1 scrambled untreated, biological rep4
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 scrambled
treatment: untreated
|
Gene expression data from endocrine resistant breast cancer cell line LY14
|
| Sample_geo_accession | GSM709776
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709776/suppl/GSM709776_S0401F014.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
GSM709777 | GPL570 |
|
LY2 control-siRNA tamoxifen treated rep4
|
LY2 cell line, SRC-1 scrambled treated 120min, biological rep4
|
cell line: LY2
phenotype: Tamoxifen resistant
knockdown: SRC-1 scrambled
treatment: tamoxifen for 120 min
|
Gene expression data from endocrine resistant breast cancer cell line LY15
|
| Sample_geo_accession | GSM709777
| | Sample_status | Public on Jan 11 2012
| | Sample_submission_date | Apr 15 2011
| | Sample_last_update_date | Jan 11 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | siRNA transfections were performed using the siPORT® Amine transfection agent according to manufacturers instructions. siRNAs used were against SRC-1 (Ambion product code: AM16706, working concentration 40nM) and scrambled control (Ambion product code 4390644 working concentration 40nM). Transfected cells were then incubated at 37oC for 24 hours prior to treatments to allow sufficient knockdown. Cells were treated with 10-7M 4-hydroxytamoxifen (treated) or vehicle control (untreated: 0.01% ethanol) for a period of 2 hours prior to RNA extraction.
| | Sample_growth_protocol_ch1 | LY2 breast cancer cells were propogated in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum and 10-8M 4-hydroxytamoxifen. Prior to treatment cells were sub-cultured for 72 hours in phenol red free MEM containing 10% charcoal dextran stripped fetal calf serum without 4-hydroxytamoxifen.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA extraction was peformed using the RNeasy® RNA extraction kit (Qiagen) according to manufacturers instructions.The RNA samples were DNase-I treated.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Total RNA was amplified using the NuGEN™ Ovation™ RNA Amplification System V2. The amplified single-stranded cDNA was purified for accurate quantitation of the cDNA and to ensure optimal performance during the fragmentation and labelling process. The appropriate amount of amplified single-stranded cDNA was fragmented and labelled using the FL-Ovation™ cDNA Biotin Module V2.
| | Sample_hyb_protocol | Fragmented and labelled cDNA was added to the hybridisation cocktail in accordance with the NuGEN™ guidelines and hybridised to Human Genome U133 Plus 2.0 GeneChip® for 16-18 hours at 45°C in an Affymetrix GeneChip® Hybridisation Oven 640.
| | Sample_scan_protocol | The array was washed and stained on the GeneChip® Fluidics Station 450 Human Genome U133 Plus 2.0 GeneChip® and scanned using the GeneChip® Scanner 3000.
| | Sample_data_processing | The data were analyzed by using R/bioconductor (R version 2.9.2) packages for differential expression genes, and ComBat.R script was used to adjust the batch effects.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Yuan,,Hao
| | Sample_contact_email | yuan.hao@ucd.ie
| | Sample_contact_institute | UCD
| | Sample_contact_address | Bioinformatics,Conway Institute, UCD
| | Sample_contact_city | Dublin
| | Sample_contact_state | Ireland
| | Sample_contact_zip/postal_code | 4
| | Sample_contact_country | Ireland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM709nnn/GSM709777/suppl/GSM709777_S0401F015.CEL.gz
| | Sample_series_id | GSE28645
| | Sample_data_row_count | 54675
| | |
|
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