Result

Search results for the GEO ID: GSE4069

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Title

Source name

Description

Characteristics

GSM93241

GPL96

oral_squamous_cell_carcinoma_49_A

oral squamous cell carcinoma

Strain/Line: CAL 27 cells,nm23-H1 transfected Cell line: oral squamous cell carcinoma Cell type: CAL 27 cells Disease state: poorly differentiated, G3 cells

Amount: 15µg fragmented cRNA Amplification: cDNA (superscript II, Invitrogen), cRNA (ENZO, one cycle)

Sample_geo_accession	GSM93241
Sample_status	Public on Aug 01 2006
Sample_submission_date	Jan 19 2006
Sample_last_update_date	Aug 01 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Laboratory for Molecular Oncology, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka 54, Zagreb, Croatia
Sample_treatment_protocol_ch1	CAL 27 cells stable transfected with pEGFP-nm23-H1 (overexpressing GFP-Nm23-H1)
Sample_growth_protocol_ch1	The experiments were conducted on human cell line CAL 27 (poorly differentiated, G3, squamous cell carcinoma of the tongue), obtained by courtesy of Dr. Jeannine Gioanni, Centre Antoine Lacassagne, Nice France). The cells were cultured in Dulbecco’s modified Eagle medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, LifeTechnologies), 2 mM glutamine, 100 U/mL penicillin and 100 ug/mL streptomycin in humidified chamber with 5% CO2, at 37oC.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	* TRIzol Reagent (Life Technologies)
Sample_extract_protocol_ch1	* RNeasy mini spin columns followed by on-column DNase digestion (Qiagen) according to manufacturer’s instructions
Sample_label_ch1	Biotinylated Oligonucleotides
Sample_hyb_protocol	1. Hybridization: 16 hours at 45°C and 60rpm, Affymetrix GeneChip Hybridization Oven 640, Affymetrix Fluidics Station 400
Sample_hyb_protocol	2. Washing and Staining:
Sample_hyb_protocol	Post Hyb Wash #1: 10 cycles of of 2 mixes/cycle with Wash Buffer A at 25°C
Sample_hyb_protocol	Post Hyb Wash #2:4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C
Sample_hyb_protocol	Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C
Sample_hyb_protocol	Post Stain Wash:10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C
Sample_hyb_protocol	2nd Stain:Stain the probe array for 10 minutes in antibody solution at 25°C
Sample_hyb_protocol	3rd Stain:Stain the probe array for 10 minutes in SAPE solution at 25°C
Sample_hyb_protocol	Final Wash:15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C
Sample_hyb_protocol	3. Buffers:
Sample_hyb_protocol	Hybridization Buffer:100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20
Sample_hyb_protocol	Wash Buffer A: Nonstringent
Sample_hyb_protocol	6x SSPE, 0.01% Tween 20
Sample_hyb_protocol	Wash Buffer B: Stringent
Sample_hyb_protocol	100 mM MES, 0.1 M [Na+], 0.01% Tween 20
Sample_hyb_protocol	Stain Buffer:100 mM MES, 1 M [Na+], 0.05% Tween 20
Sample_hyb_protocol	SAPE Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin
Sample_hyb_protocol	Antibody Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 0.1 mg/ml Normal Goat IgG, 3 μg/ml biotinylated Anti-Streptavidin
Sample_scan_protocol	Pixel Size: 3µm
Sample_scan_protocol	Filters: 570nm
Sample_scan_protocol	Number of Scans: 2
Sample_scan_protocol	Agilent GeneArray Scanner
Sample_scan_protocol	Affymetrix Microarray Suite 5.0
Sample_data_processing	MAS5.0
Sample_platform_id	GPL96
Sample_contact_name	Maja,,Herak Bosnar
Sample_contact_email	mherak@irb.hr
Sample_contact_phone	38514560997
Sample_contact_fax	38514561010
Sample_contact_laboratory	Lab. for molecular oncology
Sample_contact_department	Div. Molecular Medicine
Sample_contact_institute	Rudjer Boskovic Institute
Sample_contact_address	Bijenicka 54
Sample_contact_city	Zagreb
Sample_contact_zip/postal_code	10002
Sample_contact_country	Croatia
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM93nnn/GSM93241/suppl/GSM93241.CEL.gz
Sample_series_id	GSE4069
Sample_data_row_count	22283

GSM93242

GPL96

oral_squamous_cell_carcinoma_78_A

oral squamous cell carcinoma

Strain/Line: CAL 27 cells, empty vector transfected cells Cell line: oral squamous cell carcinoma Cell type: CAL 27 cells Disease state: poorly differentiated, G3 cells

Amount: 15µg fragmented cRNA Amplification: cDNA (superscript II, Invitrogen), cRNA (ENZO, one cycle)

Sample_geo_accession	GSM93242
Sample_status	Public on Aug 01 2006
Sample_submission_date	Jan 19 2006
Sample_last_update_date	Aug 01 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Laboratory for Molecular Oncology, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka 54, Zagreb, Croatia
Sample_treatment_protocol_ch1	CAL 27 cells stable transfected with empty vector only (overexpressing GFP)
Sample_growth_protocol_ch1	The cells were cultured in Dulbecco's modified Eagle medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, LifeTechnologies), XXX g/mL streptomycin in humidifiedm2 mM glutamine, 100 U/mL penicillin and 100 XXX chamber with 5% CO2, at 37C
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	* TRIzol Reagent (Life Technologies)
Sample_extract_protocol_ch1	* RNeasy mini spin columns followed by on-column DNase digestion (Qiagen) according to manufacturer’s instructions
Sample_label_ch1	Biotinylated Oligonucleotides
Sample_hyb_protocol	1. Hybridization: 16 hours at 45°C and 60rpm, Affymetrix GeneChip Hybridization Oven 640, Affymetrix Fluidics Station 400
Sample_hyb_protocol	2. Washing and Staining:
Sample_hyb_protocol	Post Hyb Wash #1: 10 cycles of of 2 mixes/cycle with Wash Buffer A at 25°C
Sample_hyb_protocol	Post Hyb Wash #2:4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C
Sample_hyb_protocol	Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C
Sample_hyb_protocol	Post Stain Wash:10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C
Sample_hyb_protocol	2nd Stain:Stain the probe array for 10 minutes in antibody solution at 25°C
Sample_hyb_protocol	3rd Stain:Stain the probe array for 10 minutes in SAPE solution at 25°C
Sample_hyb_protocol	Final Wash:15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C
Sample_hyb_protocol	3. Buffers:
Sample_hyb_protocol	Hybridization Buffer:100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20
Sample_hyb_protocol	Wash Buffer A: Nonstringent
Sample_hyb_protocol	6x SSPE, 0.01% Tween 20
Sample_hyb_protocol	Wash Buffer B: Stringent
Sample_hyb_protocol	100 mM MES, 0.1 M [Na+], 0.01% Tween 20
Sample_hyb_protocol	Stain Buffer:100 mM MES, 1 M [Na+], 0.05% Tween 20
Sample_hyb_protocol	SAPE Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin
Sample_hyb_protocol	Antibody Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 0.1 mg/ml Normal Goat IgG, 3 μg/ml biotinylated Anti-Streptavidin
Sample_scan_protocol	Pixel Size: 3µm
Sample_scan_protocol	Filters: 570nm
Sample_scan_protocol	Number of Scans: 2
Sample_scan_protocol	Agilent GeneArray Scanner
Sample_scan_protocol	Affymetrix Microarray Suite 5.0
Sample_data_processing	MAS5.0
Sample_platform_id	GPL96
Sample_contact_name	Maja,,Herak Bosnar
Sample_contact_email	mherak@irb.hr
Sample_contact_phone	38514560997
Sample_contact_fax	38514561010
Sample_contact_laboratory	Lab. for molecular oncology
Sample_contact_department	Div. Molecular Medicine
Sample_contact_institute	Rudjer Boskovic Institute
Sample_contact_address	Bijenicka 54
Sample_contact_city	Zagreb
Sample_contact_zip/postal_code	10002
Sample_contact_country	Croatia
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM93nnn/GSM93242/suppl/GSM93242.CEL.gz
Sample_series_id	GSE4069
Sample_data_row_count	22283

GSM151693

GPL96

oral_squamous_cell_carcinoma_71_A

oral squamous cell carcinoma

Strain/Line: CAL 27 cells transfected with pEGFPC1-nm23-H2 Cell line: oral squamous cell carcinoma Cell type: CAL 27 cells Disease state: poorly differentiated, G3 cells

Amount: 15µg fragmented cRNA Amplification: cDNA (superscript II, Invitrogen), cRNA (ENZO, one cycle)

Sample_geo_accession	GSM151693
Sample_status	Public on Dec 26 2006
Sample_submission_date	Dec 18 2006
Sample_last_update_date	Dec 26 2006
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_biomaterial_provider_ch1	Laboratory for Molecular Oncology, Division of Molecular Medicine, Rudjer Boskovic Institute, Bijenicka 54, Zagreb, Croatia
Sample_treatment_protocol_ch1	CAL 27 cells stable transfected with pEGFPC1-nm23-H2 (overexpressing nm23-H2)
Sample_growth_protocol_ch1	Cells were cultured in Dulbecco's modified Eagle medium (DMEM, Life Technologies) supplemented with 10% fetal bovine serum (FBS, Life Technologies), 100ug/mL streptomycin, 2mM glutamine, 100 U/ml penicillin in humidified chamber with 5% CO2, at 37C
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	* TRIzol Reagent (Life Technologies)
Sample_extract_protocol_ch1	* RNeasy mini spin columns followed by on-column DNase digestion (Qiagen) according to manufacturer’s instructions
Sample_label_ch1	Biotinylated Oligonucleotides
Sample_label_protocol_ch1	Biotinylated Oligonucleotides as provided in the IVT Labeling Kit (Affymetrix) following the instructions of the manufacturer.
Sample_hyb_protocol	1. Hybridization: 16 hours at 45°C and 60rpm, Affymetrix GeneChip Hybridization Oven 640, Affymetrix Fluidics Station 400
Sample_hyb_protocol	2. Washing and Staining:
Sample_hyb_protocol	Post Hyb Wash #1: 10 cycles of of 2 mixes/cycle with Wash Buffer A at 25°C
Sample_hyb_protocol	Post Hyb Wash #2:4 cycles of 15 mixes/cycle with Wash Buffer B at 50°C
Sample_hyb_protocol	Stain: Stain the probe array for 10 minutes in SAPE solution at 25°C
Sample_hyb_protocol	Post Stain Wash:10 cycles of 4 mixes/cycle with Wash Buffer A at 25°C
Sample_hyb_protocol	2nd Stain:Stain the probe array for 10 minutes in antibody solution at 25°C
Sample_hyb_protocol	3rd Stain:Stain the probe array for 10 minutes in SAPE solution at 25°C
Sample_hyb_protocol	Final Wash:15 cycles of 4 mixes/cycle with Wash Buffer A at 30°C. The holding temperature is 25°C
Sample_hyb_protocol	3. Buffers:
Sample_hyb_protocol	Hybridization Buffer:100 mM MES, 1 M [Na+], 20 mM EDTA, 0.01% Tween 20
Sample_hyb_protocol	Wash Buffer A: Nonstringent
Sample_hyb_protocol	6x SSPE, 0.01% Tween 20
Sample_hyb_protocol	Wash Buffer B: Stringent
Sample_hyb_protocol	100 mM MES, 0.1 M [Na+], 0.01% Tween 20
Sample_hyb_protocol	Stain Buffer:100 mM MES, 1 M [Na+], 0.05% Tween 20
Sample_hyb_protocol	SAPE Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 10 μg/ml Streptavidin Phycoerythrin
Sample_hyb_protocol	Antibody Solution:100 mM MES, 1 M [Na+], 0.05% Tween 20, 2 mg/ml acetylated BSA, 0.1 mg/ml Normal Goat IgG, 3 μg/ml biotinylated Anti-Streptavidin
Sample_scan_protocol	Pixel Size: 3µm
Sample_scan_protocol	Filters: 570nm
Sample_scan_protocol	Number of Scans: 2
Sample_scan_protocol	Agilent GeneArray Scanner
Sample_scan_protocol	Affymetrix Microarray Suite 5.0
Sample_data_processing	MAS5.0
Sample_platform_id	GPL96
Sample_contact_name	Maja,,Herak Bosnar
Sample_contact_email	mherak@irb.hr
Sample_contact_phone	38514560997
Sample_contact_fax	38514561010
Sample_contact_laboratory	Lab. for molecular oncology
Sample_contact_department	Div. Molecular Medicine
Sample_contact_institute	Rudjer Boskovic Institute
Sample_contact_address	Bijenicka 54
Sample_contact_city	Zagreb
Sample_contact_zip/postal_code	10002
Sample_contact_country	Croatia
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM151nnn/GSM151693/suppl/GSM151693.CEL.gz
Sample_series_id	GSE4069
Sample_data_row_count	22283

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