Result

Search results for the GEO ID: GSE17551

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM437517

GPL570

WM-266 knock-down of Pirin by siRNA - Replica 1

WM 266.4 metastatic melanoma cell line, siPIR

cell line: WM-266 pir knock-down: yes

WM-266 cells transfected with siGENOME siRNA Smartpool Reagent (Dharmacon) for knock-down of Pirin. siPIR_A

Sample_geo_accession	GSM437517
Sample_status	Public on Aug 04 2010
Sample_submission_date	Aug 06 2009
Sample_last_update_date	Aug 06 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	WM-266 cells were seeded in 6-well plates 24 hours prior to siRNA transfection. 200 pmol of siRNA oligos were transfected with Oligofectamine (Invitrogen, Carlsbad, CA) in serum-free medium. 72 hours later, cells were harvested for RNA extraction.
Sample_growth_protocol_ch1	WM-266 cells were grown in MEM medium with Glutamax supplemented with 10% FCS, 0,1mM sodium pyruvate, 0,1mM non-essential amino acids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
Sample_scan_protocol	Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
Sample_data_processing	The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Myriam,,Alcalay
Sample_contact_email	myriam.alcalay@ifom-ieo-campus.it
Sample_contact_laboratory	Functional Genomics
Sample_contact_department	Experimental Oncology
Sample_contact_institute	European Institute of Oncology
Sample_contact_address	Via Adamello 16
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20139
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437517/suppl/GSM437517.CEL.gz
Sample_series_id	GSE17551
Sample_data_row_count	54675

GSM437518

GPL570

WM-266 knock-down of Pirin by siRNA - Replica 2

WM 266.4 metastatic melanoma cell line, siPIR

cell line: WM-266 pir knock-down: yes

WM-266 cells transfected with siGENOME siRNA Smartpool Reagent (Dharmacon) for knock-down of Pirin. siPIR_B

Sample_geo_accession	GSM437518
Sample_status	Public on Aug 04 2010
Sample_submission_date	Aug 06 2009
Sample_last_update_date	Aug 06 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	WM-266 cells were seeded in 6-well plates 24 hours prior to siRNA transfection. 200 pmol of siRNA oligos were transfected with Oligofectamine (Invitrogen, Carlsbad, CA) in serum-free medium. 72 hours later, cells were harvested for RNA extraction.
Sample_growth_protocol_ch1	WM-266 cells were grown in MEM medium with Glutamax supplemented with 10% FCS, 0,1mM sodium pyruvate, 0,1mM non-essential amino acids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
Sample_scan_protocol	Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
Sample_data_processing	The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Myriam,,Alcalay
Sample_contact_email	myriam.alcalay@ifom-ieo-campus.it
Sample_contact_laboratory	Functional Genomics
Sample_contact_department	Experimental Oncology
Sample_contact_institute	European Institute of Oncology
Sample_contact_address	Via Adamello 16
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20139
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437518/suppl/GSM437518.CEL.gz
Sample_series_id	GSE17551
Sample_data_row_count	54675

GSM437519

GPL570

WM-266 cells transfected with CONTROL siRNA - Replica 1

WM 266.4 metastatic melanoma cell line, siCTR

cell line: WM-266 pir knock-down: no

WM-266 cells transfected with on-target plus siCONTROL siRNA (Dharmacon) for control. siCTR_A

Sample_geo_accession	GSM437519
Sample_status	Public on Aug 04 2010
Sample_submission_date	Aug 06 2009
Sample_last_update_date	Aug 06 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	WM-266 cells were seeded in 6-well plates 24 hours prior to siRNA transfection. 200 pmol of siRNA oligos were transfected with Oligofectamine (Invitrogen, Carlsbad, CA) in serum-free medium. 72 hours later, cells were harvested for RNA extraction.
Sample_growth_protocol_ch1	WM-266 cells were grown in MEM medium with Glutamax supplemented with 10% FCS, 0,1mM sodium pyruvate, 0,1mM non-essential amino acids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
Sample_scan_protocol	Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
Sample_data_processing	The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Myriam,,Alcalay
Sample_contact_email	myriam.alcalay@ifom-ieo-campus.it
Sample_contact_laboratory	Functional Genomics
Sample_contact_department	Experimental Oncology
Sample_contact_institute	European Institute of Oncology
Sample_contact_address	Via Adamello 16
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20139
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437519/suppl/GSM437519.CEL.gz
Sample_series_id	GSE17551
Sample_data_row_count	54675

GSM437520

GPL570

WM-266 cells transfected with CONTROL siRNA - Replica 2

WM 266.4 metastatic melanoma cell line, siCTR

cell line: WM-266 pir knock-down: no

WM-266 cells transfected with on-target plus siCONTROL siRNA (Dharmacon) for control. siCTR_B

Sample_geo_accession	GSM437520
Sample_status	Public on Aug 04 2010
Sample_submission_date	Aug 06 2009
Sample_last_update_date	Aug 06 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	WM-266 cells were seeded in 6-well plates 24 hours prior to siRNA transfection. 200 pmol of siRNA oligos were transfected with Oligofectamine (Invitrogen, Carlsbad, CA) in serum-free medium. 72 hours later, cells were harvested for RNA extraction.
Sample_growth_protocol_ch1	WM-266 cells were grown in MEM medium with Glutamax supplemented with 10% FCS, 0,1mM sodium pyruvate, 0,1mM non-essential amino acids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
Sample_scan_protocol	Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
Sample_data_processing	The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Myriam,,Alcalay
Sample_contact_email	myriam.alcalay@ifom-ieo-campus.it
Sample_contact_laboratory	Functional Genomics
Sample_contact_department	Experimental Oncology
Sample_contact_institute	European Institute of Oncology
Sample_contact_address	Via Adamello 16
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20139
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437520/suppl/GSM437520.CEL.gz
Sample_series_id	GSE17551
Sample_data_row_count	54675

GSM437521

GPL570

WM-266 cells that underwent transfection without addition of oligonucleotides - Replica 1

WM 266.4 metastatic melanoma cell line, NO

cell line: WM-266 pir knock-down: no

WM-266 cells that underwent the transfection procedure without the addition of any oligonucleotides. NO_A

Sample_geo_accession	GSM437521
Sample_status	Public on Aug 04 2010
Sample_submission_date	Aug 06 2009
Sample_last_update_date	Aug 06 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	WM-266 cells were seeded in 6-well plates 24 hours prior to siRNA transfection. 200 pmol of siRNA oligos were transfected with Oligofectamine (Invitrogen, Carlsbad, CA) in serum-free medium. 72 hours later, cells were harvested for RNA extraction.
Sample_growth_protocol_ch1	WM-266 cells were grown in MEM medium with Glutamax supplemented with 10% FCS, 0,1mM sodium pyruvate, 0,1mM non-essential amino acids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
Sample_scan_protocol	Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
Sample_data_processing	The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Myriam,,Alcalay
Sample_contact_email	myriam.alcalay@ifom-ieo-campus.it
Sample_contact_laboratory	Functional Genomics
Sample_contact_department	Experimental Oncology
Sample_contact_institute	European Institute of Oncology
Sample_contact_address	Via Adamello 16
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20139
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437521/suppl/GSM437521.CEL.gz
Sample_series_id	GSE17551
Sample_data_row_count	54675

GSM437522

GPL570

WM-266 cells that underwent transfection without addition of oligonucleotides - Replica 2

WM 266.4 metastatic melanoma cell line, NO

cell line: WM-266 pir knock-down: no

WM-266 cells that underwent the transfection procedure without the addition of any oligonucleotides. NO_B

Sample_geo_accession	GSM437522
Sample_status	Public on Aug 04 2010
Sample_submission_date	Aug 06 2009
Sample_last_update_date	Aug 06 2009
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	WM-266 cells were seeded in 6-well plates 24 hours prior to siRNA transfection. 200 pmol of siRNA oligos were transfected with Oligofectamine (Invitrogen, Carlsbad, CA) in serum-free medium. 72 hours later, cells were harvested for RNA extraction.
Sample_growth_protocol_ch1	WM-266 cells were grown in MEM medium with Glutamax supplemented with 10% FCS, 0,1mM sodium pyruvate, 0,1mM non-essential amino acids.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	Total RNA was extracted using TRIzol Reagent (Gibco), followed by clean up on RNeasy mini/midi columns (RNeasy Mini/Midi Kit, Qiagen). For each sample, an RNA pool was obtained by mixing equal quantities of total RNA from each of the three independent RNA extractions.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 ug total RNA The size and the accuracy of quantitation of targets were checked by agarose gel electrophoresis of 2ug aliquots, prior to and after fragmentation. After fragmentation, targets were diluted in hybridisation buffer at a concentration of 150ug/ml.
Sample_hyb_protocol	Following fragmentation, 12.5 ug of cRNA were hybridized for 16 hr at 45C on GeneChip GeneChip HG-U133 Plus v.2 Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station. Two copies of the GeneChip HG-U133 Plus v.2 were hybridized with each biotin-labeled target.
Sample_scan_protocol	Images were scanned using an Affymetrix GeneArray Scanner, using default parameters.
Sample_data_processing	The data were analyzed with GeneChip operating system (GCOS) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Myriam,,Alcalay
Sample_contact_email	myriam.alcalay@ifom-ieo-campus.it
Sample_contact_laboratory	Functional Genomics
Sample_contact_department	Experimental Oncology
Sample_contact_institute	European Institute of Oncology
Sample_contact_address	Via Adamello 16
Sample_contact_city	Milan
Sample_contact_zip/postal_code	20139
Sample_contact_country	Italy
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM437nnn/GSM437522/suppl/GSM437522.CEL.gz
Sample_series_id	GSE17551
Sample_data_row_count	54675

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