Result

Search results for the GEO ID: GSE41635

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Title

Source name

Description

Characteristics

GSM1020604

GPL570

MCF-7 breast cancer cell line, Control clones, 3D

Human MCF-7 breast cancer cell line, control clones in three dimension

cell line: MCF-7 genotype: control

Gene expression data from MCF-7 breast cancer cell line, control clones in three dimension

Sample_geo_accession	GSM1020604
Sample_status	Public on Oct 17 2012
Sample_submission_date	Oct 16 2012
Sample_last_update_date	Oct 17 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	MCF-7-Ctrl1, MCF-7-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells are plated into ultra-low adherence culture plates (Corning Co-Star, Tewksbury, MA) in serum-free mammary epithelial growth medium (MEBM, Lonza/Clonetics) supplemented with B27 (Invitrogen/Life Technologies Grand Island, NY), 20 ng/ml epidermal growth factor (EGF), 40 ng/ml bFGF (BD Biosciences, San Jose, CA), 4 mg/ml heparin (Sigma-Aldrich, St. Louis, MO) L-glutamine, and 100 U/ml penicillin and streptomycin. These culture conditions support self-renewal as well as formation and propagation of cells as 3 dimensional tumor spheroids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from 3 dimensional tumor spheroids of MCF-7-Ctrl1, MCF-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells was isolated using TRIzol® reagent (Invitrogen/Life Technologies Grand Island, NY), and the quality of the RNA was determined using a Nanodrop 2000 instrument (Thermo Fisher Scientific, Hanover Park, IL).
Sample_label_ch1	N/A
Sample_label_protocol_ch1	Using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA), total RNA was reverse transcripted to cDNA and synthesized to cRNA using the GeneChip® IVT Labeling kit (Affymetrix) and biotin labeled.
Sample_hyb_protocol	The cRNA was then purified using a GeneChip® Sample Cleanup Module Kit (Affymetrix) and fragmented before hybridization. Then, hybridization cocktail containing the fragmented target cRNAs and probe array controls using the GeneChip® Hybridization Control Kit (Affymetrix) was hybridized to probe array.
Sample_scan_protocol	The arrays were washed and stained according to protocol and scanned using the GeneChip® Scanner 3000 (Affymetrix).
Sample_data_processing	The data were analyzed with using DNA-Chip Analyzer software (dChip; Harvard School of Public Health, Boston, MA) using Affymetrix default analysis settings and global scaling as normalization method. dChipVersion=dChip (DNA-Chip Analyzer), Build date: Dec 17 2010.
Sample_platform_id	GPL570
Sample_contact_name	Annie,Z,Luo
Sample_contact_email	azluo@mdanderson.org
Sample_contact_phone	713-745-5516
Sample_contact_fax	713-745-9231
Sample_contact_laboratory	Dr. Robertson
Sample_contact_department	Experimental Therapeutics
Sample_contact_institute	M D Anderson Cancer Center
Sample_contact_address	1901 East Road 4SCR3.1004
Sample_contact_city	Houston
Sample_contact_state	Texas
Sample_contact_zip/postal_code	77230-1429
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1020nnn/GSM1020604/suppl/GSM1020604_MCF-7-Ctr_3D.dcp.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1020nnn/GSM1020604/suppl/GSM1020604_MCF_7_Ctr_3D.CEL.gz
Sample_series_id	GSE41635
Sample_data_row_count	54675

GSM1020605

GPL570

MCF-7 breast cancer cell line, Control clones, 3D, 2nd sample

Human MCF-7 breast cancer cell line, control clones in three dimension

cell line: MCF-7 genotype: control

Gene expression data from MCF-7 breast cancer cell line, control clones in three dimension

Sample_geo_accession	GSM1020605
Sample_status	Public on Oct 17 2012
Sample_submission_date	Oct 16 2012
Sample_last_update_date	Oct 17 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	MCF-7-Ctrl1, MCF-7-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells are plated into ultra-low adherence culture plates (Corning Co-Star, Tewksbury, MA) in serum-free mammary epithelial growth medium (MEBM, Lonza/Clonetics) supplemented with B27 (Invitrogen/Life Technologies Grand Island, NY), 20 ng/ml epidermal growth factor (EGF), 40 ng/ml bFGF (BD Biosciences, San Jose, CA), 4 mg/ml heparin (Sigma-Aldrich, St. Louis, MO) L-glutamine, and 100 U/ml penicillin and streptomycin. These culture conditions support self-renewal as well as formation and propagation of cells as 3 dimensional tumor spheroids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from 3 dimensional tumor spheroids of MCF-7-Ctrl1, MCF-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells was isolated using TRIzol® reagent (Invitrogen/Life Technologies Grand Island, NY), and the quality of the RNA was determined using a Nanodrop 2000 instrument (Thermo Fisher Scientific, Hanover Park, IL).
Sample_label_ch1	N/A
Sample_label_protocol_ch1	Using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA), total RNA was reverse transcripted to cDNA and synthesized to cRNA using the GeneChip® IVT Labeling kit (Affymetrix) and biotin labeled.
Sample_hyb_protocol	The cRNA was then purified using a GeneChip® Sample Cleanup Module Kit (Affymetrix) and fragmented before hybridization. Then, hybridization cocktail containing the fragmented target cRNAs and probe array controls using the GeneChip® Hybridization Control Kit (Affymetrix) was hybridized to probe array.
Sample_scan_protocol	The arrays were washed and stained according to protocol and scanned using the GeneChip® Scanner 3000 (Affymetrix).
Sample_data_processing	The data were analyzed with using DNA-Chip Analyzer software (dChip; Harvard School of Public Health, Boston, MA) using Affymetrix default analysis settings and global scaling as normalization method. dChipVersion=dChip (DNA-Chip Analyzer), Build date: Dec 17 2010.
Sample_platform_id	GPL570
Sample_contact_name	Annie,Z,Luo
Sample_contact_email	azluo@mdanderson.org
Sample_contact_phone	713-745-5516
Sample_contact_fax	713-745-9231
Sample_contact_laboratory	Dr. Robertson
Sample_contact_department	Experimental Therapeutics
Sample_contact_institute	M D Anderson Cancer Center
Sample_contact_address	1901 East Road 4SCR3.1004
Sample_contact_city	Houston
Sample_contact_state	Texas
Sample_contact_zip/postal_code	77230-1429
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1020nnn/GSM1020605/suppl/GSM1020605_MCF-7-Ctr_3D_2_.dcp.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1020nnn/GSM1020605/suppl/GSM1020605_MCF_7_Ctr_3D_2_.CEL.gz
Sample_series_id	GSE41635
Sample_data_row_count	54675

GSM1020606

GPL570

MCF-7 breast cancer cell line, ALK over-expressed clones, 3D

Human MCF-7 breast cancer cell line, ALK over-expressed clones in three dimension

cell line: MCF-7 genotype: ALK over-expressed clone

Gene expression data from MCF-7 breast cancer cell line, ALK over-expressed clones in three dimension

Sample_geo_accession	GSM1020606
Sample_status	Public on Oct 17 2012
Sample_submission_date	Oct 16 2012
Sample_last_update_date	Oct 17 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	MCF-7-Ctrl1, MCF-7-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells are plated into ultra-low adherence culture plates (Corning Co-Star, Tewksbury, MA) in serum-free mammary epithelial growth medium (MEBM, Lonza/Clonetics) supplemented with B27 (Invitrogen/Life Technologies Grand Island, NY), 20 ng/ml epidermal growth factor (EGF), 40 ng/ml bFGF (BD Biosciences, San Jose, CA), 4 mg/ml heparin (Sigma-Aldrich, St. Louis, MO) L-glutamine, and 100 U/ml penicillin and streptomycin. These culture conditions support self-renewal as well as formation and propagation of cells as 3 dimensional tumor spheroids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from 3 dimensional tumor spheroids of MCF-7-Ctrl1, MCF-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells was isolated using TRIzol® reagent (Invitrogen/Life Technologies Grand Island, NY), and the quality of the RNA was determined using a Nanodrop 2000 instrument (Thermo Fisher Scientific, Hanover Park, IL).
Sample_label_ch1	N/A
Sample_label_protocol_ch1	Using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA), total RNA was reverse transcripted to cDNA and synthesized to cRNA using the GeneChip® IVT Labeling kit (Affymetrix) and biotin labeled.
Sample_hyb_protocol	The cRNA was then purified using a GeneChip® Sample Cleanup Module Kit (Affymetrix) and fragmented before hybridization. Then, hybridization cocktail containing the fragmented target cRNAs and probe array controls using the GeneChip® Hybridization Control Kit (Affymetrix) was hybridized to probe array.
Sample_scan_protocol	The arrays were washed and stained according to protocol and scanned using the GeneChip® Scanner 3000 (Affymetrix).
Sample_data_processing	The data were analyzed with using DNA-Chip Analyzer software (dChip; Harvard School of Public Health, Boston, MA) using Affymetrix default analysis settings and global scaling as normalization method. dChipVersion=dChip (DNA-Chip Analyzer), Build date: Dec 17 2010.
Sample_platform_id	GPL570
Sample_contact_name	Annie,Z,Luo
Sample_contact_email	azluo@mdanderson.org
Sample_contact_phone	713-745-5516
Sample_contact_fax	713-745-9231
Sample_contact_laboratory	Dr. Robertson
Sample_contact_department	Experimental Therapeutics
Sample_contact_institute	M D Anderson Cancer Center
Sample_contact_address	1901 East Road 4SCR3.1004
Sample_contact_city	Houston
Sample_contact_state	Texas
Sample_contact_zip/postal_code	77230-1429
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1020nnn/GSM1020606/suppl/GSM1020606_MCF-7-ALK_3D.dcp.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1020nnn/GSM1020606/suppl/GSM1020606_MCF_7_ALK_3D.CEL.gz
Sample_series_id	GSE41635
Sample_data_row_count	54675

GSM1020607

GPL570

MCF-7 breast cancer cell line, ALK over-expressed clones, 3D, 2nd sample

Human MCF-7 breast cancer cell line, ALK over-expressed clones in three dimension

cell line: MCF-7 genotype: ALK over-expressed clone

Gene expression data from MCF-7 breast cancer cell line, ALK over-expressed clones in three dimension

Sample_geo_accession	GSM1020607
Sample_status	Public on Oct 17 2012
Sample_submission_date	Oct 16 2012
Sample_last_update_date	Oct 17 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_growth_protocol_ch1	MCF-7-Ctrl1, MCF-7-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells are plated into ultra-low adherence culture plates (Corning Co-Star, Tewksbury, MA) in serum-free mammary epithelial growth medium (MEBM, Lonza/Clonetics) supplemented with B27 (Invitrogen/Life Technologies Grand Island, NY), 20 ng/ml epidermal growth factor (EGF), 40 ng/ml bFGF (BD Biosciences, San Jose, CA), 4 mg/ml heparin (Sigma-Aldrich, St. Louis, MO) L-glutamine, and 100 U/ml penicillin and streptomycin. These culture conditions support self-renewal as well as formation and propagation of cells as 3 dimensional tumor spheroids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA from 3 dimensional tumor spheroids of MCF-7-Ctrl1, MCF-Ctrl2, MCF-7-ALK1 and MCF-7-ALK2 cells was isolated using TRIzol® reagent (Invitrogen/Life Technologies Grand Island, NY), and the quality of the RNA was determined using a Nanodrop 2000 instrument (Thermo Fisher Scientific, Hanover Park, IL).
Sample_label_ch1	N/A
Sample_label_protocol_ch1	Using GeneChip® One-Cycle cDNA Synthesis Kit (Affymetrix, Santa Clara, CA), total RNA was reverse transcripted to cDNA and synthesized to cRNA using the GeneChip® IVT Labeling kit (Affymetrix) and biotin labeled.
Sample_hyb_protocol	The cRNA was then purified using a GeneChip® Sample Cleanup Module Kit (Affymetrix) and fragmented before hybridization. Then, hybridization cocktail containing the fragmented target cRNAs and probe array controls using the GeneChip® Hybridization Control Kit (Affymetrix) was hybridized to probe array.
Sample_scan_protocol	The arrays were washed and stained according to protocol and scanned using the GeneChip® Scanner 3000 (Affymetrix).
Sample_data_processing	The data were analyzed with using DNA-Chip Analyzer software (dChip; Harvard School of Public Health, Boston, MA) using Affymetrix default analysis settings and global scaling as normalization method. dChipVersion=dChip (DNA-Chip Analyzer), Build date: Dec 17 2010.
Sample_platform_id	GPL570
Sample_contact_name	Annie,Z,Luo
Sample_contact_email	azluo@mdanderson.org
Sample_contact_phone	713-745-5516
Sample_contact_fax	713-745-9231
Sample_contact_laboratory	Dr. Robertson
Sample_contact_department	Experimental Therapeutics
Sample_contact_institute	M D Anderson Cancer Center
Sample_contact_address	1901 East Road 4SCR3.1004
Sample_contact_city	Houston
Sample_contact_state	Texas
Sample_contact_zip/postal_code	77230-1429
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1020nnn/GSM1020607/suppl/GSM1020607_MCF-7-ALK_3D_2_.dcp.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1020nnn/GSM1020607/suppl/GSM1020607_MCF_7_ALK_3D_2_.CEL.gz
Sample_series_id	GSE41635
Sample_data_row_count	54675

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