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Search results for the GEO ID: GSE16249

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Source name

Description

Characteristics

GSM409126

GPL570

NZM15_media_control_30hrs_rep1

NZM15 metastatic melanoma cells media-only control

tissue: skin cell line: NZM15 tumour stage: metastatic melanoma tumour site: neck nodule treatment: media-only control

Gene expression data from untreated NZM15 metastatic melanoma cells

Sample_geo_accession	GSM409126
Sample_status	Public on Jan 02 2010
Sample_submission_date	May 27 2009
Sample_last_update_date	Jan 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Sample_data_processing	The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.
Sample_platform_id	GPL570
Sample_contact_name	Aaron,,Jeffs
Sample_contact_email	aaron.jeffs@otago.ac.nz
Sample_contact_institute	University of Otago
Sample_contact_address	PO Box 56
Sample_contact_city	Dunedin
Sample_contact_zip/postal_code	9054
Sample_contact_country	New Zealand
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM409nnn/GSM409126/suppl/GSM409126.CEL.gz
Sample_series_id	GSE16249
Sample_data_row_count	54675

GSM409127

GPL570

NZM15_negative_control_30hrs_rep1

NZM15 metastatic melanoma cells treated with luciferase negative control siRNA

tissue: skin cell line: NZM15 tumour stage: metastatic melanoma tumour site: neck nodule treatment: luciferase siRNA negative control

Gene expression data from NZM15 metastatic melanoma cells treated with non-targeting negative control siRNA (luciferase)

Sample_geo_accession	GSM409127
Sample_status	Public on Jan 02 2010
Sample_submission_date	May 27 2009
Sample_last_update_date	Jan 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Sample_data_processing	The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.
Sample_platform_id	GPL570
Sample_contact_name	Aaron,,Jeffs
Sample_contact_email	aaron.jeffs@otago.ac.nz
Sample_contact_institute	University of Otago
Sample_contact_address	PO Box 56
Sample_contact_city	Dunedin
Sample_contact_zip/postal_code	9054
Sample_contact_country	New Zealand
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM409nnn/GSM409127/suppl/GSM409127.CEL.gz
Sample_series_id	GSE16249
Sample_data_row_count	54675

GSM409128

GPL570

NZM15_siMITF_30hrs_rep1

NZM15 metastatic melanoma cells treated with MITF siRNA

tissue: skin cell line: NZM15 tumour stage: metastatic melanoma tumour site: neck nodule treatment: MITF siRNA

Gene expression data from NZM15 metastatic melanoma cells treated with siRNA targeting MITF

Sample_geo_accession	GSM409128
Sample_status	Public on Jan 05 2010
Sample_submission_date	May 27 2009
Sample_last_update_date	Sep 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Sample_data_processing	The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.
Sample_platform_id	GPL570
Sample_contact_name	Aaron,,Jeffs
Sample_contact_email	aaron.jeffs@otago.ac.nz
Sample_contact_institute	University of Otago
Sample_contact_address	PO Box 56
Sample_contact_city	Dunedin
Sample_contact_zip/postal_code	9054
Sample_contact_country	New Zealand
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM409nnn/GSM409128/suppl/GSM409128.CEL.gz
Sample_series_id	GSE16249
Sample_data_row_count	54675

GSM409129

GPL570

NZM15_siPAX3_30hrs_rep1

NZM15 metastatic melanoma cells treated with PAX3 siRNA

tissue: skin cell line: NZM15 tumour stage: metastatic melanoma tumour site: neck nodule treatment: PAX3 siRNA

Gene expression data from NZM15 metastatic melanoma cells treated with siRNA targeting PAX3

Sample_geo_accession	GSM409129
Sample_status	Public on Jan 05 2010
Sample_submission_date	May 27 2009
Sample_last_update_date	Sep 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Sample_data_processing	The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.
Sample_platform_id	GPL570
Sample_contact_name	Aaron,,Jeffs
Sample_contact_email	aaron.jeffs@otago.ac.nz
Sample_contact_institute	University of Otago
Sample_contact_address	PO Box 56
Sample_contact_city	Dunedin
Sample_contact_zip/postal_code	9054
Sample_contact_country	New Zealand
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM409nnn/GSM409129/suppl/GSM409129.CEL.gz
Sample_series_id	GSE16249
Sample_data_row_count	54675

GSM409130

GPL570

NZM12_media_control_30hrs_rep1

NZM12 metastatic melanoma cells media-only control

tissue: skin cell line: NZM12 tumour stage: metastatic melanoma tumour site: small intestine treatment: media-only control

Gene expression data from untreated NZM12 metastatic melanoma cells

Sample_geo_accession	GSM409130
Sample_status	Public on Jan 02 2010
Sample_submission_date	May 27 2009
Sample_last_update_date	Jan 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Sample_data_processing	The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.
Sample_platform_id	GPL570
Sample_contact_name	Aaron,,Jeffs
Sample_contact_email	aaron.jeffs@otago.ac.nz
Sample_contact_institute	University of Otago
Sample_contact_address	PO Box 56
Sample_contact_city	Dunedin
Sample_contact_zip/postal_code	9054
Sample_contact_country	New Zealand
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM409nnn/GSM409130/suppl/GSM409130.CEL.gz
Sample_series_id	GSE16249
Sample_data_row_count	54675

GSM409131

GPL570

NZM12_negative_control_30hrs_rep1

NZM12 metastatic melanoma cells treated with luciferase negative control siRNA

tissue: skin cell line: NZM12 tumour stage: metastatic melanoma tumour site: small intestine treatment: luciferase siRNA negative control

Gene expression data from NZM12 metastatic melanoma cells treated with non-targeting negative control siRNA (luciferase)

Sample_geo_accession	GSM409131
Sample_status	Public on Jan 02 2010
Sample_submission_date	May 27 2009
Sample_last_update_date	Jan 02 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Sample_data_processing	The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.
Sample_platform_id	GPL570
Sample_contact_name	Aaron,,Jeffs
Sample_contact_email	aaron.jeffs@otago.ac.nz
Sample_contact_institute	University of Otago
Sample_contact_address	PO Box 56
Sample_contact_city	Dunedin
Sample_contact_zip/postal_code	9054
Sample_contact_country	New Zealand
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM409nnn/GSM409131/suppl/GSM409131.CEL.gz
Sample_series_id	GSE16249
Sample_data_row_count	54675

GSM409132

GPL570

NZM12_siMITF_30hrs_rep1

NZM12 metastatic melanoma cells treated with MITF siRNA

tissue: skin cell line: NZM12 tumour stage: metastatic melanoma tumour site: small intestine treatment: MITF siRNA

Gene expression data from NZM12 metastatic melanoma cells treated with siRNA targeting MITF

Sample_geo_accession	GSM409132
Sample_status	Public on Jan 05 2010
Sample_submission_date	May 27 2009
Sample_last_update_date	Sep 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Sample_data_processing	The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.
Sample_platform_id	GPL570
Sample_contact_name	Aaron,,Jeffs
Sample_contact_email	aaron.jeffs@otago.ac.nz
Sample_contact_institute	University of Otago
Sample_contact_address	PO Box 56
Sample_contact_city	Dunedin
Sample_contact_zip/postal_code	9054
Sample_contact_country	New Zealand
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM409nnn/GSM409132/suppl/GSM409132.CEL.gz
Sample_series_id	GSE16249
Sample_data_row_count	54675

GSM409133

GPL570

NZM12_siPAX3_30hrs_rep1

NZM12 metastatic melanoma cells treated with PAX3 siRNA

tissue: skin cell line: NZM12 tumour stage: metastatic melanoma tumour site: small intestine treatment: PAX3 siRNA

Gene expression data from NZM12 metastatic melanoma cells treated with siRNA targeting PAX3

Sample_geo_accession	GSM409133
Sample_status	Public on Jan 05 2010
Sample_submission_date	May 27 2009
Sample_last_update_date	Sep 13 2010
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	Reverse transfection of siRNA with a final concentration of 10 nM was performed in a 24-well plate with 30,000 cells/well by using Lipofectamine RNAiMAX (Invitrogen) according to the manufacturer's instructions. PAX3 siRNA, Ambion ID#215907, sense, GCCGCAUCCUGAGAAGUAAtt, antisense, UUACUUCUCAGGAUGCGGCtg; MITF siRNA, Ambion ID#3816, sense,GGACAAUCACAACCUGAUUtt, antisense, AAUCAGGUUGUGAUUGUCCtt; GL2 luciferase siRNA, Dharmacon Research Inc, target sequence 5'-AACGUACGCGGAAUACUUCGA-3'. Transfection efficiency determined by using the fluorescently labelled luciferase control siRNA was >90%. RNA was isolated from siRNA-treated cells and media-only controls 30 hours post-transfection.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Trizol extraction and Qiagen RNeasy column purification according to the manufacturer's instructions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared from 200 ng total RNA by using an Ambion MessageAmp Premiere kit according to the manufacturer's instructions.
Sample_hyb_protocol	Following fragmentation, 15 ug of cRNA was hybridized for 16 hr at 45°C on U133 Plus 2.0 GeneChip arrays. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the Affymetrix GeneChip Scanner 7G.
Sample_data_processing	The data was processed with the ExpressionFileCreator module of GenePattern by using the RMA method with quantile normalization and background correction.
Sample_platform_id	GPL570
Sample_contact_name	Aaron,,Jeffs
Sample_contact_email	aaron.jeffs@otago.ac.nz
Sample_contact_institute	University of Otago
Sample_contact_address	PO Box 56
Sample_contact_city	Dunedin
Sample_contact_zip/postal_code	9054
Sample_contact_country	New Zealand
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM409nnn/GSM409133/suppl/GSM409133.CEL.gz
Sample_series_id	GSE16249
Sample_data_row_count	54675

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