Result

Search results for the GEO ID: GSE29712

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM736971

GPL570

HT29_BR100_100ng_AffyExpress

HT29 BR100 RNA

cell line: HT-29 (HTB-38) cell variant: BR100 treatment: 100ng

Single sample standard labeling and hybridization

Sample_geo_accession	GSM736971
Sample_status	Public on Jun 04 2011
Sample_submission_date	Jun 03 2011
Sample_last_update_date	Jun 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HT-29 cells were cultured with continuous presence of bortezomib by stepwise increases in concentration (20 nM to 300 nM) over 7 months. Clonal isolates were derived by 2 separate limiting dilution analysis in 96-well plates under constant bortezomib exposure of 100 nM or 300 nM for an additional 4 months.
Sample_growth_protocol_ch1	HT-29 cells (American Type Culture Collection, Manassas, VA) were cultured in 37°C incubators with 5% CO2, using McCoy’s 5a with L-glutamine and supplemented with 10% fetal bovine serum (FBS), 2.2g/l sodium bicarbonate, 100 units/ml penicillin, 100 units/ml streptomycin and 1.5g/l D-glucose.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from cells using TRIzol (Invitrogen) in combination with PureLink Micro-to-Midi RNA columns (Invitrogen) using the manufacturers protocol. RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	3 ug of Total RNA was labeled using the One-Cycle Target Labeling kit and 100 ng of Total RNA was labeled using the 3' IVT Express kit from Affymetrix as per the manufacturers suggestion
Sample_hyb_protocol	Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol
Sample_scan_protocol	Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer
Sample_data_processing	Signal estimates were generated in R/Bioconductor using the GCRMA package with default settings
Sample_platform_id	GPL570
Sample_contact_name	Jonathan,J,Keats
Sample_contact_email	jkeats@tgen.org
Sample_contact_phone	602-343-8690
Sample_contact_fax	602-343-8740
Sample_contact_laboratory	Multiple Myeloma Research Lab - Keats Lab
Sample_contact_department	Integrated Cancer Genomics
Sample_contact_institute	Translational Genomics Research Institute (TGen)
Sample_contact_address	445 N. Fifth Street
Sample_contact_city	Phoenix
Sample_contact_state	Arizona
Sample_contact_zip/postal_code	85004
Sample_contact_country	Canada
Sample_contact_web_link	www.tgen.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM736nnn/GSM736971/suppl/GSM736971.cel.gz
Sample_series_id	GSE29712
Sample_series_id	GSE29713
Sample_data_row_count	54675

GSM736972

GPL570

HT29_BR100_3ug_AffyOneStep

HT29 BR100 RNA

cell line: HT-29 (HTB-38) cell variant: BR100 treatment: 3ug

Single sample standard labeling and hybridization

Sample_geo_accession	GSM736972
Sample_status	Public on Jun 04 2011
Sample_submission_date	Jun 03 2011
Sample_last_update_date	Jun 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HT-29 cells were cultured with continuous presence of bortezomib by stepwise increases in concentration (20 nM to 300 nM) over 7 months. Clonal isolates were derived by 2 separate limiting dilution analysis in 96-well plates under constant bortezomib exposure of 100 nM or 300 nM for an additional 4 months.
Sample_growth_protocol_ch1	HT-29 cells (American Type Culture Collection, Manassas, VA) were cultured in 37°C incubators with 5% CO2, using McCoy’s 5a with L-glutamine and supplemented with 10% fetal bovine serum (FBS), 2.2g/l sodium bicarbonate, 100 units/ml penicillin, 100 units/ml streptomycin and 1.5g/l D-glucose.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from cells using TRIzol (Invitrogen) in combination with PureLink Micro-to-Midi RNA columns (Invitrogen) using the manufacturers protocol. RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	3 ug of Total RNA was labeled using the One-Cycle Target Labeling kit and 100 ng of Total RNA was labeled using the 3' IVT Express kit from Affymetrix as per the manufacturers suggestion
Sample_hyb_protocol	Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol
Sample_scan_protocol	Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer
Sample_data_processing	Signal estimates were generated in R/Bioconductor using the GCRMA package with default settings
Sample_platform_id	GPL570
Sample_contact_name	Jonathan,J,Keats
Sample_contact_email	jkeats@tgen.org
Sample_contact_phone	602-343-8690
Sample_contact_fax	602-343-8740
Sample_contact_laboratory	Multiple Myeloma Research Lab - Keats Lab
Sample_contact_department	Integrated Cancer Genomics
Sample_contact_institute	Translational Genomics Research Institute (TGen)
Sample_contact_address	445 N. Fifth Street
Sample_contact_city	Phoenix
Sample_contact_state	Arizona
Sample_contact_zip/postal_code	85004
Sample_contact_country	Canada
Sample_contact_web_link	www.tgen.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM736nnn/GSM736972/suppl/GSM736972.cel.gz
Sample_series_id	GSE29712
Sample_series_id	GSE29713
Sample_data_row_count	54675

GSM736973

GPL570

HT29_BR200_100ng_AffyExpress

HT29 BR200 RNA

cell line: HT-29 (HTB-38) cell variant: BR200 treatment: 100ng

Single sample standard labeling and hybridization

Sample_geo_accession	GSM736973
Sample_status	Public on Jun 04 2011
Sample_submission_date	Jun 03 2011
Sample_last_update_date	Jun 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HT-29 cells were cultured with continuous presence of bortezomib by stepwise increases in concentration (20 nM to 300 nM) over 7 months. Clonal isolates were derived by 2 separate limiting dilution analysis in 96-well plates under constant bortezomib exposure of 100 nM or 300 nM for an additional 4 months.
Sample_growth_protocol_ch1	HT-29 cells (American Type Culture Collection, Manassas, VA) were cultured in 37°C incubators with 5% CO2, using McCoy’s 5a with L-glutamine and supplemented with 10% fetal bovine serum (FBS), 2.2g/l sodium bicarbonate, 100 units/ml penicillin, 100 units/ml streptomycin and 1.5g/l D-glucose.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from cells using TRIzol (Invitrogen) in combination with PureLink Micro-to-Midi RNA columns (Invitrogen) using the manufacturers protocol. RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	3 ug of Total RNA was labeled using the One-Cycle Target Labeling kit and 100 ng of Total RNA was labeled using the 3' IVT Express kit from Affymetrix as per the manufacturers suggestion
Sample_hyb_protocol	Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol
Sample_scan_protocol	Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer
Sample_data_processing	Signal estimates were generated in R/Bioconductor using the GCRMA package with default settings
Sample_platform_id	GPL570
Sample_contact_name	Jonathan,J,Keats
Sample_contact_email	jkeats@tgen.org
Sample_contact_phone	602-343-8690
Sample_contact_fax	602-343-8740
Sample_contact_laboratory	Multiple Myeloma Research Lab - Keats Lab
Sample_contact_department	Integrated Cancer Genomics
Sample_contact_institute	Translational Genomics Research Institute (TGen)
Sample_contact_address	445 N. Fifth Street
Sample_contact_city	Phoenix
Sample_contact_state	Arizona
Sample_contact_zip/postal_code	85004
Sample_contact_country	Canada
Sample_contact_web_link	www.tgen.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM736nnn/GSM736973/suppl/GSM736973.cel.gz
Sample_series_id	GSE29712
Sample_series_id	GSE29713
Sample_data_row_count	54675

GSM736974

GPL570

HT29_BR200_3ug_AffyOneStep

HT29 BR200 RNA

cell line: HT-29 (HTB-38) cell variant: BR200 treatment: 3ug

Single sample standard labeling and hybridization

Sample_geo_accession	GSM736974
Sample_status	Public on Jun 04 2011
Sample_submission_date	Jun 03 2011
Sample_last_update_date	Jun 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HT-29 cells were cultured with continuous presence of bortezomib by stepwise increases in concentration (20 nM to 300 nM) over 7 months. Clonal isolates were derived by 2 separate limiting dilution analysis in 96-well plates under constant bortezomib exposure of 100 nM or 300 nM for an additional 4 months.
Sample_growth_protocol_ch1	HT-29 cells (American Type Culture Collection, Manassas, VA) were cultured in 37°C incubators with 5% CO2, using McCoy’s 5a with L-glutamine and supplemented with 10% fetal bovine serum (FBS), 2.2g/l sodium bicarbonate, 100 units/ml penicillin, 100 units/ml streptomycin and 1.5g/l D-glucose.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from cells using TRIzol (Invitrogen) in combination with PureLink Micro-to-Midi RNA columns (Invitrogen) using the manufacturers protocol. RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	3 ug of Total RNA was labeled using the One-Cycle Target Labeling kit and 100 ng of Total RNA was labeled using the 3' IVT Express kit from Affymetrix as per the manufacturers suggestion
Sample_hyb_protocol	Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol
Sample_scan_protocol	Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer
Sample_data_processing	Signal estimates were generated in R/Bioconductor using the GCRMA package with default settings
Sample_platform_id	GPL570
Sample_contact_name	Jonathan,J,Keats
Sample_contact_email	jkeats@tgen.org
Sample_contact_phone	602-343-8690
Sample_contact_fax	602-343-8740
Sample_contact_laboratory	Multiple Myeloma Research Lab - Keats Lab
Sample_contact_department	Integrated Cancer Genomics
Sample_contact_institute	Translational Genomics Research Institute (TGen)
Sample_contact_address	445 N. Fifth Street
Sample_contact_city	Phoenix
Sample_contact_state	Arizona
Sample_contact_zip/postal_code	85004
Sample_contact_country	Canada
Sample_contact_web_link	www.tgen.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM736nnn/GSM736974/suppl/GSM736974.cel.gz
Sample_series_id	GSE29712
Sample_series_id	GSE29713
Sample_data_row_count	54675

GSM736975

GPL570

HT29_wildtype_100ng_AffyExpress

HT29 Wildtype RNA

cell line: HT-29 (HTB-38) cell variant: wild type treatment: 100ng

Single sample standard labeling and hybridization

Sample_geo_accession	GSM736975
Sample_status	Public on Jun 04 2011
Sample_submission_date	Jun 03 2011
Sample_last_update_date	Jun 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HT-29 cells were cultured with continuous presence of bortezomib by stepwise increases in concentration (20 nM to 300 nM) over 7 months. Clonal isolates were derived by 2 separate limiting dilution analysis in 96-well plates under constant bortezomib exposure of 100 nM or 300 nM for an additional 4 months.
Sample_growth_protocol_ch1	HT-29 cells (American Type Culture Collection, Manassas, VA) were cultured in 37°C incubators with 5% CO2, using McCoy’s 5a with L-glutamine and supplemented with 10% fetal bovine serum (FBS), 2.2g/l sodium bicarbonate, 100 units/ml penicillin, 100 units/ml streptomycin and 1.5g/l D-glucose.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from cells using TRIzol (Invitrogen) in combination with PureLink Micro-to-Midi RNA columns (Invitrogen) using the manufacturers protocol. RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	3 ug of Total RNA was labeled using the One-Cycle Target Labeling kit and 100 ng of Total RNA was labeled using the 3' IVT Express kit from Affymetrix as per the manufacturers suggestion
Sample_hyb_protocol	Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol
Sample_scan_protocol	Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer
Sample_data_processing	Signal estimates were generated in R/Bioconductor using the GCRMA package with default settings
Sample_platform_id	GPL570
Sample_contact_name	Jonathan,J,Keats
Sample_contact_email	jkeats@tgen.org
Sample_contact_phone	602-343-8690
Sample_contact_fax	602-343-8740
Sample_contact_laboratory	Multiple Myeloma Research Lab - Keats Lab
Sample_contact_department	Integrated Cancer Genomics
Sample_contact_institute	Translational Genomics Research Institute (TGen)
Sample_contact_address	445 N. Fifth Street
Sample_contact_city	Phoenix
Sample_contact_state	Arizona
Sample_contact_zip/postal_code	85004
Sample_contact_country	Canada
Sample_contact_web_link	www.tgen.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM736nnn/GSM736975/suppl/GSM736975.cel.gz
Sample_series_id	GSE29712
Sample_series_id	GSE29713
Sample_data_row_count	54675

GSM736976

GPL570

HT29_wildtype_3ug_AffyOneStep

HT29 Wildtype RNA

cell line: HT-29 (HTB-38) cell variant: wild type treatment: 3ug

Single sample standard labeling and hybridization

Sample_geo_accession	GSM736976
Sample_status	Public on Jun 04 2011
Sample_submission_date	Jun 03 2011
Sample_last_update_date	Jun 04 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	HT-29 cells were cultured with continuous presence of bortezomib by stepwise increases in concentration (20 nM to 300 nM) over 7 months. Clonal isolates were derived by 2 separate limiting dilution analysis in 96-well plates under constant bortezomib exposure of 100 nM or 300 nM for an additional 4 months.
Sample_growth_protocol_ch1	HT-29 cells (American Type Culture Collection, Manassas, VA) were cultured in 37°C incubators with 5% CO2, using McCoy’s 5a with L-glutamine and supplemented with 10% fetal bovine serum (FBS), 2.2g/l sodium bicarbonate, 100 units/ml penicillin, 100 units/ml streptomycin and 1.5g/l D-glucose.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNA was extracted from cells using TRIzol (Invitrogen) in combination with PureLink Micro-to-Midi RNA columns (Invitrogen) using the manufacturers protocol. RNA samples were tested for purity and concentration on a Nanodrop spectrophotometer and quality checked on an Agilent Bioanalyzer
Sample_label_ch1	biotin
Sample_label_protocol_ch1	3 ug of Total RNA was labeled using the One-Cycle Target Labeling kit and 100 ng of Total RNA was labeled using the 3' IVT Express kit from Affymetrix as per the manufacturers suggestion
Sample_hyb_protocol	Labeled cRNA was hybridized to U133Plus2.0 GeneChips in a GeneChip Hybridization Oven 640 and washed using a GeneChip Fluidics Station 450 as per the manufacturers protocol
Sample_scan_protocol	Arrays were scanned using a GeneChip Scanner 3000 following the recommendations of the manufacturer
Sample_data_processing	Signal estimates were generated in R/Bioconductor using the GCRMA package with default settings
Sample_platform_id	GPL570
Sample_contact_name	Jonathan,J,Keats
Sample_contact_email	jkeats@tgen.org
Sample_contact_phone	602-343-8690
Sample_contact_fax	602-343-8740
Sample_contact_laboratory	Multiple Myeloma Research Lab - Keats Lab
Sample_contact_department	Integrated Cancer Genomics
Sample_contact_institute	Translational Genomics Research Institute (TGen)
Sample_contact_address	445 N. Fifth Street
Sample_contact_city	Phoenix
Sample_contact_state	Arizona
Sample_contact_zip/postal_code	85004
Sample_contact_country	Canada
Sample_contact_web_link	www.tgen.org
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM736nnn/GSM736976/suppl/GSM736976.cel.gz
Sample_series_id	GSE29712
Sample_series_id	GSE29713
Sample_data_row_count	54675

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