Result

Search results for the GEO ID: GSE26462

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GSM ID

GPL ID

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Title

Source name

Description

Characteristics

GSM650467

GPL570

231-knockdown-rep 1

WASF3 knockdown single clone 1

cell line: MDA-MB-231 passage 4, puromycin resistant

highly aggressive cancer cell line

Sample_geo_accession	GSM650467
Sample_status	Public on Jan 06 2011
Sample_submission_date	Jan 05 2011
Sample_last_update_date	Jan 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	To generate WASF3 stable knockdown MDA-MB-231 cells, the pSM2 retroviral vectors containing a short hairpin RNA against WASF3 (shRNA1 - V2LHS 261688; shRNA2-V2LHS90825; Open Biosystems, Huntsville, AL) were used for infection. As controls the empty pSM2 vector and an shRNA targeting GFP, were used. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and individual drug-resistant clones were collected and expanded.
Sample_growth_protocol_ch1	MDA-MB-231 cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNAs were extracted using Trizol reagent (Invitrogen) and the Qiagen RNeasy kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using a Bioanalyzer to assess the quality of the sample.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).The probe was generated using the Affymetrix 3’ IVT Express protocol.
Sample_hyb_protocol	All samples passing this quality control were hybridized to a GeneChip® Human Genome U133A 2.0 Array (Affymetrix, CA) probing 18,400 transcripts and variants. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450 (x2) .
Sample_scan_protocol	GeneChips were scanned using the Affymetrix® GeneChip Scanner 3000 7G Plus
Sample_data_processing	The data were analyzed with Affymetrix Expression Console Software (v.1.0) using Affymetrix default analysis settings and global scaling as normalization method (RMA). The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	yong,,teng
Sample_contact_email	gzyteng@yahoo.com.cn
Sample_contact_institute	Medical College of Georgia
Sample_contact_address	1120 15th Street
Sample_contact_city	Augusta
Sample_contact_zip/postal_code	30912
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650467/suppl/GSM650467.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650467/suppl/GSM650467.chp.gz
Sample_series_id	GSE26462
Sample_data_row_count	54675

GSM650468

GPL570

231-knockdown-rep 2

WASF3 knockdown single clone 2

cell line: MDA-MB-231 passage 4, puromycin resistant

highly aggressive cancer cell line

Sample_geo_accession	GSM650468
Sample_status	Public on Jan 06 2011
Sample_submission_date	Jan 05 2011
Sample_last_update_date	Jan 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	To generate WASF3 stable knockdown MDA-MB-231 cells, the pSM2 retroviral vectors containing a short hairpin RNA against WASF3 (shRNA1 - V2LHS 261688; shRNA2-V2LHS90825; Open Biosystems, Huntsville, AL) were used for infection. As controls the empty pSM2 vector and an shRNA targeting GFP, were used. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and individual drug-resistant clones were collected and expanded.
Sample_growth_protocol_ch1	MDA-MB-231 cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNAs were extracted using Trizol reagent (Invitrogen) and the Qiagen RNeasy kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using a Bioanalyzer to assess the quality of the sample.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).The probe was generated using the Affymetrix 3’ IVT Express protocol.
Sample_hyb_protocol	All samples passing this quality control were hybridized to a GeneChip® Human Genome U133A 2.0 Array (Affymetrix, CA) probing 18,400 transcripts and variants. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450 (x2) .
Sample_scan_protocol	GeneChips were scanned using the Affymetrix® GeneChip Scanner 3000 7G Plus
Sample_data_processing	The data were analyzed with Affymetrix Expression Console Software (v.1.0) using Affymetrix default analysis settings and global scaling as normalization method (RMA). The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	yong,,teng
Sample_contact_email	gzyteng@yahoo.com.cn
Sample_contact_institute	Medical College of Georgia
Sample_contact_address	1120 15th Street
Sample_contact_city	Augusta
Sample_contact_zip/postal_code	30912
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650468/suppl/GSM650468.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650468/suppl/GSM650468.chp.gz
Sample_series_id	GSE26462
Sample_data_row_count	54675

GSM650469

GPL570

231-knockdown-rep 3

WASF3 knockdown single clone 3

cell line: MDA-MB-231 passage 4, puromycin resistant

highly aggressive cancer cell line

Sample_geo_accession	GSM650469
Sample_status	Public on Jan 06 2011
Sample_submission_date	Jan 05 2011
Sample_last_update_date	Jan 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	To generate WASF3 stable knockdown MDA-MB-231 cells, the pSM2 retroviral vectors containing a short hairpin RNA against WASF3 (shRNA1 - V2LHS 261688; shRNA2-V2LHS90825; Open Biosystems, Huntsville, AL) were used for infection. As controls the empty pSM2 vector and an shRNA targeting GFP, were used. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and individual drug-resistant clones were collected and expanded.
Sample_growth_protocol_ch1	MDA-MB-231 cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNAs were extracted using Trizol reagent (Invitrogen) and the Qiagen RNeasy kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using a Bioanalyzer to assess the quality of the sample.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).The probe was generated using the Affymetrix 3’ IVT Express protocol.
Sample_hyb_protocol	All samples passing this quality control were hybridized to a GeneChip® Human Genome U133A 2.0 Array (Affymetrix, CA) probing 18,400 transcripts and variants. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450 (x2) .
Sample_scan_protocol	GeneChips were scanned using the Affymetrix® GeneChip Scanner 3000 7G Plus
Sample_data_processing	The data were analyzed with Affymetrix Expression Console Software (v.1.0) using Affymetrix default analysis settings and global scaling as normalization method (RMA). The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	yong,,teng
Sample_contact_email	gzyteng@yahoo.com.cn
Sample_contact_institute	Medical College of Georgia
Sample_contact_address	1120 15th Street
Sample_contact_city	Augusta
Sample_contact_zip/postal_code	30912
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650469/suppl/GSM650469.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650469/suppl/GSM650469.chp.gz
Sample_series_id	GSE26462
Sample_data_row_count	54675

GSM650470

GPL570

231-control-rep 1

control single clone 1

cell line: MDA-MB-231 passage 4, puromycin resistant

highly aggressive cancer cell line

Sample_geo_accession	GSM650470
Sample_status	Public on Jan 06 2011
Sample_submission_date	Jan 05 2011
Sample_last_update_date	Jan 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	To generate WASF3 stable knockdown MDA-MB-231 cells, the pSM2 retroviral vectors containing a short hairpin RNA against WASF3 (shRNA1 - V2LHS 261688; shRNA2-V2LHS90825; Open Biosystems, Huntsville, AL) were used for infection. As controls the empty pSM2 vector and an shRNA targeting GFP, were used. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and individual drug-resistant clones were collected and expanded.
Sample_growth_protocol_ch1	MDA-MB-231 cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNAs were extracted using Trizol reagent (Invitrogen) and the Qiagen RNeasy kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using a Bioanalyzer to assess the quality of the sample.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).The probe was generated using the Affymetrix 3’ IVT Express protocol.
Sample_hyb_protocol	All samples passing this quality control were hybridized to a GeneChip® Human Genome U133A 2.0 Array (Affymetrix, CA) probing 18,400 transcripts and variants. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450 (x2) .
Sample_scan_protocol	GeneChips were scanned using the Affymetrix® GeneChip Scanner 3000 7G Plus
Sample_data_processing	The data were analyzed with Affymetrix Expression Console Software (v.1.0) using Affymetrix default analysis settings and global scaling as normalization method (RMA). The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	yong,,teng
Sample_contact_email	gzyteng@yahoo.com.cn
Sample_contact_institute	Medical College of Georgia
Sample_contact_address	1120 15th Street
Sample_contact_city	Augusta
Sample_contact_zip/postal_code	30912
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650470/suppl/GSM650470.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650470/suppl/GSM650470.chp.gz
Sample_series_id	GSE26462
Sample_data_row_count	54675

GSM650471

GPL570

231-control-rep 2

control single clone 2

cell line: MDA-MB-231 passage 4, puromycin resistant

highly aggressive cancer cell line

Sample_geo_accession	GSM650471
Sample_status	Public on Jan 06 2011
Sample_submission_date	Jan 05 2011
Sample_last_update_date	Jan 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	To generate WASF3 stable knockdown MDA-MB-231 cells, the pSM2 retroviral vectors containing a short hairpin RNA against WASF3 (shRNA1 - V2LHS 261688; shRNA2-V2LHS90825; Open Biosystems, Huntsville, AL) were used for infection. As controls the empty pSM2 vector and an shRNA targeting GFP, were used. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and individual drug-resistant clones were collected and expanded.
Sample_growth_protocol_ch1	MDA-MB-231 cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNAs were extracted using Trizol reagent (Invitrogen) and the Qiagen RNeasy kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using a Bioanalyzer to assess the quality of the sample.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).The probe was generated using the Affymetrix 3’ IVT Express protocol.
Sample_hyb_protocol	All samples passing this quality control were hybridized to a GeneChip® Human Genome U133A 2.0 Array (Affymetrix, CA) probing 18,400 transcripts and variants. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450 (x2) .
Sample_scan_protocol	GeneChips were scanned using the Affymetrix® GeneChip Scanner 3000 7G Plus
Sample_data_processing	The data were analyzed with Affymetrix Expression Console Software (v.1.0) using Affymetrix default analysis settings and global scaling as normalization method (RMA). The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	yong,,teng
Sample_contact_email	gzyteng@yahoo.com.cn
Sample_contact_institute	Medical College of Georgia
Sample_contact_address	1120 15th Street
Sample_contact_city	Augusta
Sample_contact_zip/postal_code	30912
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650471/suppl/GSM650471.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650471/suppl/GSM650471.chp.gz
Sample_series_id	GSE26462
Sample_data_row_count	54675

GSM650472

GPL570

231-control-rep 3

control single clone 3

cell line: MDA-MB-231 passage 4, puromycin resistant

highly aggressive cancer cell line

Sample_geo_accession	GSM650472
Sample_status	Public on Jan 06 2011
Sample_submission_date	Jan 05 2011
Sample_last_update_date	Jan 06 2011
Sample_type	RNA
Sample_channel_count	1
Sample_organism_ch1	Homo sapiens
Sample_taxid_ch1	9606
Sample_treatment_protocol_ch1	To generate WASF3 stable knockdown MDA-MB-231 cells, the pSM2 retroviral vectors containing a short hairpin RNA against WASF3 (shRNA1 - V2LHS 261688; shRNA2-V2LHS90825; Open Biosystems, Huntsville, AL) were used for infection. As controls the empty pSM2 vector and an shRNA targeting GFP, were used. Virally infected cells were selected in a medium containing 1.0 μg/ml puromycin (Sigma, NY) for 2 weeks and individual drug-resistant clones were collected and expanded.
Sample_growth_protocol_ch1	MDA-MB-231 cells were purchased from the American Type Culture Collection (Rockville, MD) and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS).
Sample_molecule_ch1	total RNA
Sample_extract_protocol_ch1	RNAs were extracted using Trizol reagent (Invitrogen) and the Qiagen RNeasy kit (Qiagen, CA) according to manufacturer’s instructions and then evaluated using a Bioanalyzer to assess the quality of the sample.
Sample_label_ch1	biotin
Sample_label_protocol_ch1	Biotinylated cDNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).The probe was generated using the Affymetrix 3’ IVT Express protocol.
Sample_hyb_protocol	All samples passing this quality control were hybridized to a GeneChip® Human Genome U133A 2.0 Array (Affymetrix, CA) probing 18,400 transcripts and variants. GeneChips were washed and stained in the Affymetrix® Fluidics Station 450 (x2) .
Sample_scan_protocol	GeneChips were scanned using the Affymetrix® GeneChip Scanner 3000 7G Plus
Sample_data_processing	The data were analyzed with Affymetrix Expression Console Software (v.1.0) using Affymetrix default analysis settings and global scaling as normalization method (RMA). The trimmed mean target intensity of each array was arbitrarily set to 100.
Sample_platform_id	GPL570
Sample_contact_name	yong,,teng
Sample_contact_email	gzyteng@yahoo.com.cn
Sample_contact_institute	Medical College of Georgia
Sample_contact_address	1120 15th Street
Sample_contact_city	Augusta
Sample_contact_zip/postal_code	30912
Sample_contact_country	USA
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650472/suppl/GSM650472.CEL.gz
Sample_supplementary_file	ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM650nnn/GSM650472/suppl/GSM650472.chp.gz
Sample_series_id	GSE26462
Sample_data_row_count	54675

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