Result

Search results for the GEO ID: GSE18370

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GPL ID

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Title

Source name

Description

Characteristics

GSM458329

GPL570

PTci bio rep 1

ADH

cell ine: PTci

cell line PTci, First Biological replicate. represents ADH

Sample_geo_accession	GSM458329
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458329/suppl/GSM458329_AFFY1236.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458329/suppl/GSM458329_AFFY1236.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

GSM458330

GPL570

PTci bio rep 2

ADH

cell ine: PTci

cell line PTci, Second Biological replicate. represents ADH

Sample_geo_accession	GSM458330
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458330/suppl/GSM458330_AFFY1287.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458330/suppl/GSM458330_AFFY1287.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

GSM458331

GPL570

PTci bio rep 3

ADH

cell ine: PTci

cell line PTci, Third Biological replicate. represents ADH

Sample_geo_accession	GSM458331
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458331/suppl/GSM458331_AFFY1291.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458331/suppl/GSM458331_AFFY1291.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

GSM458332

GPL570

NTci bio rep 1

DCIS

cell ine: NTci

cell line NTci, First Biological replicate. represents DCIS

Sample_geo_accession	GSM458332
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458332/suppl/GSM458332_AFFY1237.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458332/suppl/GSM458332_AFFY1237.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

GSM458333

GPL570

NTci bio rep 2

DCIS

cell ine: NTci

cell line NTci, Second Biological replicate. represents DCIS

Sample_geo_accession	GSM458333
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458333/suppl/GSM458333_AFFY1289.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458333/suppl/GSM458333_AFFY1289.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

GSM458334

GPL570

NTci bio rep 3

DCIS

cell ine: NTci

cell line NTci, Third Biological replicate. represents DCIS

Sample_geo_accession	GSM458334
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458334/suppl/GSM458334_AFFY1288.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458334/suppl/GSM458334_AFFY1288.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

GSM458335

GPL570

MT1 Bio rep 1

IDC

cell ine: MT-1

cell line MT1, First Biological replicate. represents IDC

Sample_geo_accession	GSM458335
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458335/suppl/GSM458335_AFFY1238.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458335/suppl/GSM458335_AFFY1238.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

GSM458336

GPL570

MT1 Bio rep 2

IDC

cell ine: MT-1

cell line MT1, Second Biological replicate. represents IDC

Sample_geo_accession	GSM458336
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458336/suppl/GSM458336_AFFY1292.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458336/suppl/GSM458336_AFFY1292.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

GSM458337

GPL570

MT1 Bio rep 3

IDC

cell ine: MT-1

cell line MT1, Third Biological replicate. represents IDC

Sample_geo_accession	GSM458337
Sample_status	Public on Mar 09 2010
Sample_submission_date	Oct 01 2009
Sample_last_update_date	Mar 09 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	No treatment
Sample_growth_protocol_ch1	For all 3D cultures, 21PTci, 21NTci and 21MT-1 cells were grown in Matrigel Basement Membrane Matrix (BD Biosciences, Mississauga, ON) for 9 days. Cultures were created in 24-well plates (Nunc, VWR International, Mississauga, ON) with three distinct layers. The bottom layer consisted of undiluted Matrigel for a solid base. The middle layer contained a 1:1 mix of Matrigel and 2 x 105 cells in media supplemented with 0.1% BSA, instead of FBS. These two layers were topped with growth media supplemented with 0.1% BSA (without FBS)
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Three wells per cell line, representing 3 biological replicates, were grown. Total RNA from each biological replicate was isolated using Cell Recovery Solution (BD Biosciences, Mississauga, ON) to non-enzymatically dissociate the Matrigel, followed by TRIzol (Invitrogen), as per the manufacturer's instructions
Sample_label_ch1	Biotin/SAPE
Sample_label_protocol_ch1	Ligation mediated PCR amplified genomic DNA, after restriction with HhaI, was labeled as per Affymetrix standard protocol for Human Promoter 1.0R arrays
Sample_hyb_protocol	cRNA was synthesized and Biotin labeled as per the array manufacturer's instructions (www.affymetrix.com). Arrays were washed, stained with Streptavidin-phycoerythrin, washed again, and scanned
Sample_scan_protocol	GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
Sample_data_processing	Washing, scanning and probe quantification were carried out according to the manufacturer's instructions, using GeneChip Operating Software (GCOS, www.affymetrix.com), with target intensity set to 150. For each array, GCOS output was imported as .txt files into Genespring GX 7.3 software (Agilent), and data were normalized as follows: Values <0.01 were set to 0.01 and the median intensity of each array was normalized to the 50th percentile of all arrays. Finally, the intensity of each probe set in each of the three 21NTci or 21MT-1 arrays was divided by the normalized mean intensity of that probe set in the control arrays.
Sample_platform_id	GPL570
Sample_contact_name	Ann,,Chambers
Sample_contact_email	joseph.andrews@lhsc.on.ca
Sample_contact_phone	(519) 685-8430
Sample_contact_department	Victoria research labs
Sample_contact_institute	London Regional Cancer program
Sample_contact_address	790 Commissioner's Road E
Sample_contact_city	London
Sample_contact_state	Ontario
Sample_contact_zip/postal_code	N6A 4L6
Sample_contact_country	Canada
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458337/suppl/GSM458337_AFFY1290.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM458nnn/GSM458337/suppl/GSM458337_AFFY1290.CHP.gz
Sample_series_id	GSE18370
Sample_data_row_count	54675

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