Result

Search results for the GEO ID: GSE10289

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM259831

GPL570

pU62_A

hepatocellular carcinoma cell line Hep3B cells, plasmid pU6, clone 2

Hep3B cells stably transfected with short hairpin vectors (plasmid pU6 is the host vector) Hep3B cells stably transfected with plasmid pU6, clone 2, replicate 1

Gene expression data from control cell line

Sample_geo_accession	GSM259831
Sample_status	Public on Apr 01 2008
Sample_submission_date	Jan 28 2008
Sample_last_update_date	Feb 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cell lines were grown until nearly confluent, washed in PBS, and scraped off in PBS using a cell scraper. Cells were collected by centrifugation before RNA extraction.
Sample_growth_protocol_ch1	cell lines were grown in MEM medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-Glutamine, 1mM non-essential aminoacids, 1 mM sodium pyruvate and 400 µg/ml G418. Cell cultures were propagated at 37 ºC in a humidified 5% CO2, 95% air atmosphere.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was extracted from pelleted cells using the RNeasy minikit from Qiagen.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
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 TGT intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Manolo,,Mata
Sample_contact_email	manuel.mata@uv.es
Sample_contact_phone	(34)963864639
Sample_contact_laboratory	Affymetrix
Sample_contact_department	UCIM
Sample_contact_institute	university of valencia
Sample_contact_address	Avda. Blasco Ibanez, 17
Sample_contact_city	Valencia
Sample_contact_zip/postal_code	46010
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259831/suppl/GSM259831.CEL.gz
Sample_series_id	GSE10289
Sample_data_row_count	54675

GSM259832

GPL570

pU62_B

hepatocellular carcinoma cell line Hep3B cells, plasmid pU6, clone 2

Hep3B cells stably transfected with short hairpin vectors (plasmid pU6 is the host vector) Hep3B cells stably transfected with plasmid pU6, clone 2, replicate 2

Gene expression data from control cell line

Sample_geo_accession	GSM259832
Sample_status	Public on Apr 01 2008
Sample_submission_date	Jan 28 2008
Sample_last_update_date	Feb 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cell lines were grown until nearly confluent, washed in PBS, and scraped off in PBS using a cell scraper. Cells were collected by centrifugation before RNA extraction.
Sample_growth_protocol_ch1	cell lines were grown in MEM medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-Glutamine, 1mM non-essential aminoacids, 1 mM sodium pyruvate and 400 µg/ml G418. Cell cultures were propagated at 37 ºC in a humidified 5% CO2, 95% air atmosphere.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was extracted from pelleted cells using the RNeasy minikit from Qiagen.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
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 TGT intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Manolo,,Mata
Sample_contact_email	manuel.mata@uv.es
Sample_contact_phone	(34)963864639
Sample_contact_laboratory	Affymetrix
Sample_contact_department	UCIM
Sample_contact_institute	university of valencia
Sample_contact_address	Avda. Blasco Ibanez, 17
Sample_contact_city	Valencia
Sample_contact_zip/postal_code	46010
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259832/suppl/GSM259832.CEL.gz
Sample_series_id	GSE10289
Sample_data_row_count	54675

GSM259833

GPL570

pU62_C

hepatocellular carcinoma cell line Hep3B cells, plasmid pU6, clone 2

Hep3B cells stably transfected with short hairpin vectors (plasmid pU6 is the host vector) Hep3B cells stably transfected with plasmid pU6, clone 2, replicate 3

Gene expression data from control cell line

Sample_geo_accession	GSM259833
Sample_status	Public on Apr 01 2008
Sample_submission_date	Jan 28 2008
Sample_last_update_date	Feb 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cell lines were grown until nearly confluent, washed in PBS, and scraped off in PBS using a cell scraper. Cells were collected by centrifugation before RNA extraction.
Sample_growth_protocol_ch1	cell lines were grown in MEM medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-Glutamine, 1mM non-essential aminoacids, 1 mM sodium pyruvate and 400 µg/ml G418. Cell cultures were propagated at 37 ºC in a humidified 5% CO2, 95% air atmosphere.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was extracted from pelleted cells using the RNeasy minikit from Qiagen.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
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 TGT intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Manolo,,Mata
Sample_contact_email	manuel.mata@uv.es
Sample_contact_phone	(34)963864639
Sample_contact_laboratory	Affymetrix
Sample_contact_department	UCIM
Sample_contact_institute	university of valencia
Sample_contact_address	Avda. Blasco Ibanez, 17
Sample_contact_city	Valencia
Sample_contact_zip/postal_code	46010
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259833/suppl/GSM259833.CEL.gz
Sample_series_id	GSE10289
Sample_data_row_count	54675

GSM259834

GPL570

D20_A

hepatocellular carcinoma cell line Hep3B cells, plasmid siSDHB, clone D20

Hep3B cells stably transfected with short hairpin vectors containing an siRNA directed to SDHB Hep3B cells stably transfected with plasmid siSDHB, clone D20, replicate 1

Gene expression data from cell line knocked-down for SDHB gene

Sample_geo_accession	GSM259834
Sample_status	Public on Apr 01 2008
Sample_submission_date	Jan 28 2008
Sample_last_update_date	Feb 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cell lines were grown until nearly confluent, washed in PBS, and scraped off in PBS using a cell scraper. Cells were collected by centrifugation before RNA extraction.
Sample_growth_protocol_ch1	cell lines were grown in MEM medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-Glutamine, 1mM non-essential aminoacids, 1 mM sodium pyruvate and 400 µg/ml G418. Cell cultures were propagated at 37 ºC in a humidified 5% CO2, 95% air atmosphere.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was extracted from pelleted cells using the RNeasy minikit from Qiagen.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
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 TGT intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Manolo,,Mata
Sample_contact_email	manuel.mata@uv.es
Sample_contact_phone	(34)963864639
Sample_contact_laboratory	Affymetrix
Sample_contact_department	UCIM
Sample_contact_institute	university of valencia
Sample_contact_address	Avda. Blasco Ibanez, 17
Sample_contact_city	Valencia
Sample_contact_zip/postal_code	46010
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259834/suppl/GSM259834.CEL.gz
Sample_series_id	GSE10289
Sample_data_row_count	54675

GSM259835

GPL570

D20_B

hepatocellular carcinoma cell line Hep3B cells, plasmid siSDHB, clone D20

Hep3B cells stably transfected with short hairpin vectors containing an siRNA directed to SDHB Hep3B cells stably transfected with plasmid siSDHB, clone D20, replicate 2

Gene expression data from cell line knocked-down for SDHB gene

Sample_geo_accession	GSM259835
Sample_status	Public on Apr 01 2008
Sample_submission_date	Jan 28 2008
Sample_last_update_date	Feb 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cell lines were grown until nearly confluent, washed in PBS, and scraped off in PBS using a cell scraper. Cells were collected by centrifugation before RNA extraction.
Sample_growth_protocol_ch1	cell lines were grown in MEM medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-Glutamine, 1mM non-essential aminoacids, 1 mM sodium pyruvate and 400 µg/ml G418. Cell cultures were propagated at 37 ºC in a humidified 5% CO2, 95% air atmosphere.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was extracted from pelleted cells using the RNeasy minikit from Qiagen.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
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 TGT intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Manolo,,Mata
Sample_contact_email	manuel.mata@uv.es
Sample_contact_phone	(34)963864639
Sample_contact_laboratory	Affymetrix
Sample_contact_department	UCIM
Sample_contact_institute	university of valencia
Sample_contact_address	Avda. Blasco Ibanez, 17
Sample_contact_city	Valencia
Sample_contact_zip/postal_code	46010
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259835/suppl/GSM259835.CEL.gz
Sample_series_id	GSE10289
Sample_data_row_count	54675

GSM259836

GPL570

D20_C

hepatocellular carcinoma cell line Hep3B cells, plasmid siSDHB, clone D20

Hep3B cells stably transfected with short hairpin vectors containing an siRNA directed to SDHB Hep3B cells stably transfected with plasmid siSDHB, clone D20, replicate 3

Gene expression data from cell line knocked-down for SDHB gene

Sample_geo_accession	GSM259836
Sample_status	Public on Apr 01 2008
Sample_submission_date	Jan 28 2008
Sample_last_update_date	Feb 22 2008
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	cell lines were grown until nearly confluent, washed in PBS, and scraped off in PBS using a cell scraper. Cells were collected by centrifugation before RNA extraction.
Sample_growth_protocol_ch1	cell lines were grown in MEM medium supplemented with 10% heat-inactivated fetal bovine serum, 2mM L-Glutamine, 1mM non-essential aminoacids, 1 mM sodium pyruvate and 400 µg/ml G418. Cell cultures were propagated at 37 ºC in a humidified 5% CO2, 95% air atmosphere.
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	total RNA was extracted from pelleted cells using the RNeasy minikit from Qiagen.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
Sample_hyb_protocol	Following fragmentation, 15 microg of cRNA were hybridized for 16 hr at 45C on Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Sample_scan_protocol	GeneChips were scanned using the GeneChip Scanner 3000.
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 TGT intensity of each array was arbitrarily set to 500.
Sample_platform_id	GPL570
Sample_contact_name	Manolo,,Mata
Sample_contact_email	manuel.mata@uv.es
Sample_contact_phone	(34)963864639
Sample_contact_laboratory	Affymetrix
Sample_contact_department	UCIM
Sample_contact_institute	university of valencia
Sample_contact_address	Avda. Blasco Ibanez, 17
Sample_contact_city	Valencia
Sample_contact_zip/postal_code	46010
Sample_contact_country	Spain
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM259nnn/GSM259836/suppl/GSM259836.CEL.gz
Sample_series_id	GSE10289
Sample_data_row_count	54675

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