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Search results for the GEO ID: GSE30684

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(Once the selection is made, click on "Add groups" in "Make groups for comparison", to make a group. Scroll down)

GSM ID

GPL ID

Select for analysis

Title

Source name

Description

Characteristics

GSM761172

GPL1261

shLuc-treated Wnt1-YL cells, biological rep 1

shLuc shRNA control treatment

cell line: Wnt1-YL tissue: derived from primary MMTV-Wnt1 mammary tumors

shLuc shRNA control treatment in mouse mammary tumor cell line (Wnt1-YL), rep 1

Sample_geo_accession	GSM761172
Sample_status	Public on Feb 16 2012
Sample_submission_date	Jul 14 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Mouse mammary tumor cell line (Wnt1-YL), derived from primary MMTV-Wnt1 breast tumors. The cells were grown in DMEM/F12 (Invitrogen) at ph7.6, with 2% adult bovine serum (Gemini Bio-Products), antibiotic/antimycotic (invitrogen), 5 μg/ml gentimycin (Sigma), 10 μg/ml insulin (invitrogen) and 5 ng/mL EGF (invitrogen).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM761nnn/GSM761172/suppl/GSM761172_Wnt_Luc_1.cel.gz
Sample_series_id	GSE30684
Sample_data_row_count	45101

GSM761173

GPL1261

shLuc-treated Wnt1-YL cells, biological rep 2

shLuc shRNA control treatment

cell line: Wnt1-YL tissue: derived from primary MMTV-Wnt1 mammary tumors

shLuc shRNA control treatment in mouse mammary tumor cell line (Wnt1-YL), rep 2

Sample_geo_accession	GSM761173
Sample_status	Public on Feb 16 2012
Sample_submission_date	Jul 14 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Mouse mammary tumor cell line (Wnt1-YL), derived from primary MMTV-Wnt1 breast tumors. The cells were grown in DMEM/F12 (Invitrogen) at ph7.6, with 2% adult bovine serum (Gemini Bio-Products), antibiotic/antimycotic (invitrogen), 5 μg/ml gentimycin (Sigma), 10 μg/ml insulin (invitrogen) and 5 ng/mL EGF (invitrogen).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM761nnn/GSM761173/suppl/GSM761173_Wnt_Luc_2.cel.gz
Sample_series_id	GSE30684
Sample_data_row_count	45101

GSM761174

GPL1261

shLuc-treated Wnt1-YL cells, biological rep 3

shLuc shRNA control treatment

cell line: Wnt1-YL tissue: derived from primary MMTV-Wnt1 mammary tumors

shLuc shRNA control treatment in mouse mammary tumor cell line (Wnt1-YL), rep 3

Sample_geo_accession	GSM761174
Sample_status	Public on Feb 16 2012
Sample_submission_date	Jul 14 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Mouse mammary tumor cell line (Wnt1-YL), derived from primary MMTV-Wnt1 breast tumors. The cells were grown in DMEM/F12 (Invitrogen) at ph7.6, with 2% adult bovine serum (Gemini Bio-Products), antibiotic/antimycotic (invitrogen), 5 μg/ml gentimycin (Sigma), 10 μg/ml insulin (invitrogen) and 5 ng/mL EGF (invitrogen).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM761nnn/GSM761174/suppl/GSM761174_Wnt_Luc_3.cel.gz
Sample_series_id	GSE30684
Sample_data_row_count	45101

GSM761175

GPL1261

shSca-1-treated Wnt1-YL cells, biological rep 1

knockdown of Sca-1 by shRNA

cell line: Wnt1-YL tissue: derived from primary MMTV-Wnt1 mammary tumors

knockdown of Sca-1 by shRNA in mouse mammary tumor cell line (Wnt1-YL), rep 1

Sample_geo_accession	GSM761175
Sample_status	Public on Feb 16 2012
Sample_submission_date	Jul 14 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Mouse mammary tumor cell line (Wnt1-YL), derived from primary MMTV-Wnt1 breast tumors. The cells were grown in DMEM/F12 (Invitrogen) at ph7.6, with 2% adult bovine serum (Gemini Bio-Products), antibiotic/antimycotic (invitrogen), 5 μg/ml gentimycin (Sigma), 10 μg/ml insulin (invitrogen) and 5 ng/mL EGF (invitrogen).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM761nnn/GSM761175/suppl/GSM761175_Wnt_Sca_1_1.cel.gz
Sample_series_id	GSE30684
Sample_data_row_count	45101

GSM761176

GPL1261

shSca-1-treated Wnt1-YL cells, biological rep 2

knockdown of Sca-1 by shRNA

cell line: Wnt1-YL tissue: derived from primary MMTV-Wnt1 mammary tumors

knockdown of Sca-1 by shRNA in mouse mammary tumor cell line (Wnt1-YL), rep 2

Sample_geo_accession	GSM761176
Sample_status	Public on Feb 16 2012
Sample_submission_date	Jul 14 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Mouse mammary tumor cell line (Wnt1-YL), derived from primary MMTV-Wnt1 breast tumors. The cells were grown in DMEM/F12 (Invitrogen) at ph7.6, with 2% adult bovine serum (Gemini Bio-Products), antibiotic/antimycotic (invitrogen), 5 μg/ml gentimycin (Sigma), 10 μg/ml insulin (invitrogen) and 5 ng/mL EGF (invitrogen).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM761nnn/GSM761176/suppl/GSM761176_Wnt_Sca_1_2.cel.gz
Sample_series_id	GSE30684
Sample_data_row_count	45101

GSM761177

GPL1261

shSca-1-treated Wnt1-YL cells, biological rep 3

knockdown of Sca-1 by shRNA

cell line: Wnt1-YL tissue: derived from primary MMTV-Wnt1 mammary tumors

knockdown of Sca-1 by shRNA in mouse mammary tumor cell line (Wnt1-YL), rep 3

Sample_geo_accession	GSM761177
Sample_status	Public on Feb 16 2012
Sample_submission_date	Jul 14 2011
Sample_last_update_date	Feb 16 2012
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Mus musculus
Sample_taxid_ch1	10090
Sample_growth_protocol_ch1	Mouse mammary tumor cell line (Wnt1-YL), derived from primary MMTV-Wnt1 breast tumors. The cells were grown in DMEM/F12 (Invitrogen) at ph7.6, with 2% adult bovine serum (Gemini Bio-Products), antibiotic/antimycotic (invitrogen), 5 μg/ml gentimycin (Sigma), 10 μg/ml insulin (invitrogen) and 5 ng/mL EGF (invitrogen).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was isolated from cells using TRIzol Reagent (Invitrogen) and then cDNA was made from total RNA with SuperScript II (Invitrogen) using random primers. cDNA was treated with RNase H (Invitrogen) to remove RNA.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA were hybridized on Mouse430_2 GeneChip following the recommended procedures. GeneChips were washed and stained according to Affymetrix protocol EukGE-WS2v5 (for FS400) or FS450_0001 (for FS450).
Sample_scan_protocol	GeneChips were scanned using an Affymetrix GeneChip Scanner (Agilent).
Sample_data_processing	The data were analyzed with dChip version2006 using Affymetrix default analysis settings and invariant set normalization method.
Sample_platform_id	GPL1261
Sample_contact_name	Chad,,Creighton
Sample_contact_email	creighto@bcm.tmc.edu
Sample_contact_department	Biostatistics, Ducan Cancer Center
Sample_contact_institute	Baylor College of Medicine
Sample_contact_address	One Baylor Plaza, Mail Stop: BCM305
Sample_contact_city	Houston
Sample_contact_state	TX
Sample_contact_zip/postal_code	77030
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM761nnn/GSM761177/suppl/GSM761177_Wnt_Sca_1_3.cel.gz
Sample_series_id	GSE30684
Sample_data_row_count	45101

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