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Search results for the GEO ID: GSE14337

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Description

Characteristics

GSM358693

GPL1355

MUC1-CD-transfected 3Y1 cells grown in vitro, biological replicate 1

MUC1-CD-transfected 3Y1 cells grown in vitro

transformed embryonic fibroblasts

gene expression data from MUC1-CD-transfected 3Y1 cells grown in vitro

Sample_geo_accession	GSM358693
Sample_status	Public on Apr 10 2009
Sample_submission_date	Jan 08 2009
Sample_last_update_date	Apr 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Tumors were excised, snap-frozen in liquid nitrogen, and stored at -80 ˚C. Frozen xenografts were sectioned into pieces approximately 5 mm^3 in size and soaked overnight in RNAlater®-ICE solution (Applied Biosystems-Ambion, Austin, TX, USA). Samples were spun, washed in RLT buffer (QIAGEN, Valencia, CA, USA) and homogenized on ice using a mechanical glass-Teflon homogenizer set at 3000 rpm. Further purification was performed using a combination of RNeasy spin columns and TRIzol reagent, as previously described (PMID: 11848408).
Sample_growth_protocol_ch1	Rat 3Y1 embryonic fibroblasts were stably transfected by an empty vector (3Y1/Vector) or one expressing the cytoplasmic domain of MUC1 (3Y1/MUC1-CD) as previously described (PMID: 16288032). Transfected 3Y1 cells were cultured in DMEM media with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mmol/L L-glutamine and maintained at 37 ˚C in a humidified environment containing 5% CO2. 3Y1/Vector and 3Y1/MUC1-CD cells were injected subcutaneously into the hindlimbs of female athymic mice (FCRI-Taconic, Frederick, MD) in increasing concentrations from 10^2 to 10^7 cells in 100 µl of PBS per mouse. Mice were euthanized using CO2 followed by cervical dislocation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on GeneChip® Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700.
Sample_platform_id	GPL1355
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358693/suppl/GSM358693.CEL.gz
Sample_series_id	GSE14337
Sample_data_row_count	31099

GSM358694

GPL1355

MUC1-CD-transfected 3Y1 cells grown in vitro, biological replicate 2

MUC1-CD-transfected 3Y1 cells grown in vitro

transformed embryonic fibroblasts

gene expression data from MUC1-CD-transfected 3Y1 cells grown in vitro

Sample_geo_accession	GSM358694
Sample_status	Public on Apr 10 2009
Sample_submission_date	Jan 08 2009
Sample_last_update_date	Apr 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Tumors were excised, snap-frozen in liquid nitrogen, and stored at -80 ˚C. Frozen xenografts were sectioned into pieces approximately 5 mm^3 in size and soaked overnight in RNAlater®-ICE solution (Applied Biosystems-Ambion, Austin, TX, USA). Samples were spun, washed in RLT buffer (QIAGEN, Valencia, CA, USA) and homogenized on ice using a mechanical glass-Teflon homogenizer set at 3000 rpm. Further purification was performed using a combination of RNeasy spin columns and TRIzol reagent, as previously described (PMID: 11848408).
Sample_growth_protocol_ch1	Rat 3Y1 embryonic fibroblasts were stably transfected by an empty vector (3Y1/Vector) or one expressing the cytoplasmic domain of MUC1 (3Y1/MUC1-CD) as previously described (PMID: 16288032). Transfected 3Y1 cells were cultured in DMEM media with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mmol/L L-glutamine and maintained at 37 ˚C in a humidified environment containing 5% CO2. 3Y1/Vector and 3Y1/MUC1-CD cells were injected subcutaneously into the hindlimbs of female athymic mice (FCRI-Taconic, Frederick, MD) in increasing concentrations from 10^2 to 10^7 cells in 100 µl of PBS per mouse. Mice were euthanized using CO2 followed by cervical dislocation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on GeneChip® Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700.
Sample_platform_id	GPL1355
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358694/suppl/GSM358694.CEL.gz
Sample_series_id	GSE14337
Sample_data_row_count	31099

GSM358695

GPL1355

MUC1-CD-transfected 3Y1 cells grown in vivo, biological replicate 1

MUC1-CD-transfected 3Y1 cells grown in vivo

transformed embryonic fibroblasts

gene expression data from MUC1-CD-transfected 3Y1 cells grown in vivo

Sample_geo_accession	GSM358695
Sample_status	Public on Apr 10 2009
Sample_submission_date	Jan 08 2009
Sample_last_update_date	Apr 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Tumors were excised, snap-frozen in liquid nitrogen, and stored at -80 ˚C. Frozen xenografts were sectioned into pieces approximately 5 mm^3 in size and soaked overnight in RNAlater®-ICE solution (Applied Biosystems-Ambion, Austin, TX, USA). Samples were spun, washed in RLT buffer (QIAGEN, Valencia, CA, USA) and homogenized on ice using a mechanical glass-Teflon homogenizer set at 3000 rpm. Further purification was performed using a combination of RNeasy spin columns and TRIzol reagent, as previously described (PMID: 11848408).
Sample_growth_protocol_ch1	Rat 3Y1 embryonic fibroblasts were stably transfected by an empty vector (3Y1/Vector) or one expressing the cytoplasmic domain of MUC1 (3Y1/MUC1-CD) as previously described (PMID: 16288032). Transfected 3Y1 cells were cultured in DMEM media with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mmol/L L-glutamine and maintained at 37 ˚C in a humidified environment containing 5% CO2. 3Y1/Vector and 3Y1/MUC1-CD cells were injected subcutaneously into the hindlimbs of female athymic mice (FCRI-Taconic, Frederick, MD) in increasing concentrations from 10^2 to 10^7 cells in 100 µl of PBS per mouse. Mice were euthanized using CO2 followed by cervical dislocation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on GeneChip® Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700.
Sample_platform_id	GPL1355
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358695/suppl/GSM358695.CEL.gz
Sample_series_id	GSE14337
Sample_data_row_count	31099

GSM358696

GPL1355

MUC1-CD-transfected 3Y1 cells grown in vivo, biological replicate 2

MUC1-CD-transfected 3Y1 cells grown in vivo

transformed embryonic fibroblasts

gene expression data from MUC1-CD-transfected 3Y1 cells grown in vivo

Sample_geo_accession	GSM358696
Sample_status	Public on Apr 10 2009
Sample_submission_date	Jan 08 2009
Sample_last_update_date	Apr 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Tumors were excised, snap-frozen in liquid nitrogen, and stored at -80 ˚C. Frozen xenografts were sectioned into pieces approximately 5 mm^3 in size and soaked overnight in RNAlater®-ICE solution (Applied Biosystems-Ambion, Austin, TX, USA). Samples were spun, washed in RLT buffer (QIAGEN, Valencia, CA, USA) and homogenized on ice using a mechanical glass-Teflon homogenizer set at 3000 rpm. Further purification was performed using a combination of RNeasy spin columns and TRIzol reagent, as previously described (PMID: 11848408).
Sample_growth_protocol_ch1	Rat 3Y1 embryonic fibroblasts were stably transfected by an empty vector (3Y1/Vector) or one expressing the cytoplasmic domain of MUC1 (3Y1/MUC1-CD) as previously described (PMID: 16288032). Transfected 3Y1 cells were cultured in DMEM media with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mmol/L L-glutamine and maintained at 37 ˚C in a humidified environment containing 5% CO2. 3Y1/Vector and 3Y1/MUC1-CD cells were injected subcutaneously into the hindlimbs of female athymic mice (FCRI-Taconic, Frederick, MD) in increasing concentrations from 10^2 to 10^7 cells in 100 µl of PBS per mouse. Mice were euthanized using CO2 followed by cervical dislocation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on GeneChip® Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700.
Sample_platform_id	GPL1355
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358696/suppl/GSM358696.CEL.gz
Sample_series_id	GSE14337
Sample_data_row_count	31099

GSM358697

GPL1355

Empty vector-transfected 3Y1 cells grown in vitro, biological replicate 1

Empty vector-transfected 3Y1 cells grown in vitro

non-transformed embryonic fibroblasts

gene expression data from empty vector-transfected 3Y1 cells grown in vitro

Sample_geo_accession	GSM358697
Sample_status	Public on Apr 10 2009
Sample_submission_date	Jan 08 2009
Sample_last_update_date	Apr 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Tumors were excised, snap-frozen in liquid nitrogen, and stored at -80 ˚C. Frozen xenografts were sectioned into pieces approximately 5 mm^3 in size and soaked overnight in RNAlater®-ICE solution (Applied Biosystems-Ambion, Austin, TX, USA). Samples were spun, washed in RLT buffer (QIAGEN, Valencia, CA, USA) and homogenized on ice using a mechanical glass-Teflon homogenizer set at 3000 rpm. Further purification was performed using a combination of RNeasy spin columns and TRIzol reagent, as previously described (PMID: 11848408).
Sample_growth_protocol_ch1	Rat 3Y1 embryonic fibroblasts were stably transfected by an empty vector (3Y1/Vector) or one expressing the cytoplasmic domain of MUC1 (3Y1/MUC1-CD) as previously described (PMID: 16288032). Transfected 3Y1 cells were cultured in DMEM media with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mmol/L L-glutamine and maintained at 37 ˚C in a humidified environment containing 5% CO2. 3Y1/Vector and 3Y1/MUC1-CD cells were injected subcutaneously into the hindlimbs of female athymic mice (FCRI-Taconic, Frederick, MD) in increasing concentrations from 10^2 to 10^7 cells in 100 µl of PBS per mouse. Mice were euthanized using CO2 followed by cervical dislocation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on GeneChip® Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700.
Sample_platform_id	GPL1355
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358697/suppl/GSM358697.CEL.gz
Sample_series_id	GSE14337
Sample_data_row_count	31099

GSM358698

GPL1355

Empty vector-transfected 3Y1 cells grown in vitro, biological replicate 2

Empty vector-transfected 3Y1 cells grown in vitro

non-transformed embryonic fibroblasts

gene expression data from empty vector-transfected 3Y1 cells grown in vitro

Sample_geo_accession	GSM358698
Sample_status	Public on Apr 10 2009
Sample_submission_date	Jan 08 2009
Sample_last_update_date	Apr 10 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Rattus norvegicus
Sample_taxid_ch1	10116
Sample_treatment_protocol_ch1	Tumors were excised, snap-frozen in liquid nitrogen, and stored at -80 ˚C. Frozen xenografts were sectioned into pieces approximately 5 mm^3 in size and soaked overnight in RNAlater®-ICE solution (Applied Biosystems-Ambion, Austin, TX, USA). Samples were spun, washed in RLT buffer (QIAGEN, Valencia, CA, USA) and homogenized on ice using a mechanical glass-Teflon homogenizer set at 3000 rpm. Further purification was performed using a combination of RNeasy spin columns and TRIzol reagent, as previously described (PMID: 11848408).
Sample_growth_protocol_ch1	Rat 3Y1 embryonic fibroblasts were stably transfected by an empty vector (3Y1/Vector) or one expressing the cytoplasmic domain of MUC1 (3Y1/MUC1-CD) as previously described (PMID: 16288032). Transfected 3Y1 cells were cultured in DMEM media with 10% heat-inactivated fetal bovine serum, 100 units/mL penicillin, 100 µg/mL streptomycin, and 2 mmol/L L-glutamine and maintained at 37 ˚C in a humidified environment containing 5% CO2. 3Y1/Vector and 3Y1/MUC1-CD cells were injected subcutaneously into the hindlimbs of female athymic mice (FCRI-Taconic, Frederick, MD) in increasing concentrations from 10^2 to 10^7 cells in 100 µl of PBS per mouse. Mice were euthanized using CO2 followed by cervical dislocation.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	TRIzol extraction of total RNA was performed according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 10 ug of cRNA were hybridized on GeneChip® Rat Genome 230 2.0 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
Sample_scan_protocol	GeneChips were scanned using the Agilent GeneArray Scanner.
Sample_data_processing	The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 700.
Sample_platform_id	GPL1355
Sample_contact_name	Sean,Pravin,Pitroda
Sample_contact_email	spitroda@uchicago.edu
Sample_contact_department	Radiation and Cellular Oncology
Sample_contact_institute	The University of Chicago
Sample_contact_address	5841 South Maryland Avenue, MC 1105
Sample_contact_city	Chicago
Sample_contact_state	IL
Sample_contact_zip/postal_code	60637
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM358nnn/GSM358698/suppl/GSM358698.CEL.gz
Sample_series_id	GSE14337
Sample_data_row_count	31099

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