Search results for the GEO ID: GSE33950 |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM839353 | GPL570 |
|
MDA shGFP, biological replicate A
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), untreated
|
genotype/variation: control cells
|
Gene expression data from control MDA-MB-231 cells
|
Sample_geo_accession | GSM839353
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839353/suppl/GSM839353.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839354 | GPL570 |
|
MDA shGFP, biological replicate B
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), untreated
|
genotype/variation: control cells
|
Gene expression data from control MDA-MB-231 cells
|
Sample_geo_accession | GSM839354
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839354/suppl/GSM839354.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839355 | GPL570 |
|
MDA shGFP, biological replicate C
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), untreated
|
genotype/variation: control cells
|
Gene expression data from control MDA-MB-231 cells
|
Sample_geo_accession | GSM839355
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839355/suppl/GSM839355.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839356 | GPL570 |
|
MDA shGFP, biological replicate D
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), untreated
|
genotype/variation: control cells
|
Gene expression data from control MDA-MB-231 cells
|
Sample_geo_accession | GSM839356
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839356/suppl/GSM839356.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839357 | GPL570 |
|
MDA shHIF, biological replicate A
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), treated with TGFbeta (5ug/ml) for 3 hrs.
|
genotype/variation: cells depleted of HIF1a and HIF2a
|
Gene expression data from MDA-MB-231 cells depleted of HIF1a and HIF2a
|
Sample_geo_accession | GSM839357
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839357/suppl/GSM839357.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839358 | GPL570 |
|
MDA shHIF, biological replicate B
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), treated with TGFbeta (5ug/ml) for 3 hrs.
|
genotype/variation: cells depleted of HIF1a and HIF2a
|
Gene expression data from MDA-MB-231 cells depleted of HIF1a and HIF2a
|
Sample_geo_accession | GSM839358
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839358/suppl/GSM839358.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839359 | GPL570 |
|
MDA shHIF, biological replicate C
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), treated with TGFbeta (5ug/ml) for 3 hrs.
|
genotype/variation: cells depleted of HIF1a and HIF2a
|
Gene expression data from MDA-MB-231 cells depleted of HIF1a and HIF2a
|
Sample_geo_accession | GSM839359
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839359/suppl/GSM839359.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839360 | GPL570 |
|
MDA shHIF, biological replicate D
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against GFP (shGFP), treated with TGFbeta (5ug/ml) for 3 hrs.
|
genotype/variation: cells depleted of HIF1a and HIF2a
|
Gene expression data from MDA-MB-231 cells depleted of HIF1a and HIF2a
|
Sample_geo_accession | GSM839360
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839360/suppl/GSM839360.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839361 | GPL570 |
|
MDA Sharp1, biological replicate A
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against TP53 (shp53), untreated
|
genotype/variation: cells overexpressing Sharp1
|
Gene expression data from Sharp1-overexpressing MDA-MB-231 cells
|
Sample_geo_accession | GSM839361
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839361/suppl/GSM839361.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839362 | GPL570 |
|
MDA Sharp1, biological replicate B
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against TP53 (shp53), untreated
|
genotype/variation: cells overexpressing Sharp1
|
Gene expression data from Sharp1-overexpressing MDA-MB-231 cells
|
Sample_geo_accession | GSM839362
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839362/suppl/GSM839362.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839363 | GPL570 |
|
MDA Sharp1, biological replicate C
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against TP53 (shp53), untreated
|
genotype/variation: cells overexpressing Sharp1
|
Gene expression data from Sharp1-overexpressing MDA-MB-231 cells
|
Sample_geo_accession | GSM839363
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839363/suppl/GSM839363.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
GSM839364 | GPL570 |
|
MDA Sharp1, biological replicate D
|
human metastatic breast cell line MDA-MB-231, infected with a Retroviral construct expressing small-hairpin RNA against TP53 (shp53), untreated
|
genotype/variation: cells overexpressing Sharp1
|
Gene expression data from Sharp1-overexpressing MDA-MB-231 cells
|
Sample_geo_accession | GSM839364
| Sample_status | Public on Jul 19 2012
| Sample_submission_date | Nov 25 2011
| Sample_last_update_date | Jul 19 2012
| Sample_type | RNA
| Sample_channel_count | 1
| Sample_organism_ch1 | Homo sapiens
| Sample_taxid_ch1 | 9606
| Sample_treatment_protocol_ch1 | Cells were cultivated under normal growing conditions
| Sample_growth_protocol_ch1 | MDA-MB-231 were maintained in a 1:1 mixture of DMEM and F12 (DMEM/F12) supplemented with 10% serum and 2 mM glutamine.
| Sample_molecule_ch1 | total RNA
| Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| Sample_label_ch1 | biotin
| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared using the BioArrayTM HighYieldTM RNA Transcript Labeling Kit (ENZO Biochem, New York, NY) according to manufacturer's intructions.
| Sample_hyb_protocol | Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome HG-U133 Plus 2.0 arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
| Sample_scan_protocol | Standard Affymetrix scanning procedures on a GCS3000 7G Affymetrix scanner operated by GCOS, GeneChip Operating Software
| Sample_data_processing | RMA of .CEL files using affy Bioconductor library. In RMA, PM values have been background adjusted, normalized using quantile normalization, and expression measure calculated using median polish summarization
| Sample_platform_id | GPL570
| Sample_contact_name | Silvio,,Bicciato
| Sample_contact_email | silvio.bicciato@unimore.it
| Sample_contact_phone | +39-059-205-5219
| Sample_contact_fax | +39-029-205-5410
| Sample_contact_laboratory | Center for Genome Research
| Sample_contact_department | Life Sciences
| Sample_contact_institute | University of Modena and Reggio Emilia
| Sample_contact_address | via Campi, 287
| Sample_contact_city | Modena
| Sample_contact_zip/postal_code | 41100
| Sample_contact_country | Italy
| Sample_contact_web_link | http://www.cgr.unimore.it/cgi-bin/cgr/persone.pl/Show?_id=sbicciat&sort=DEFAULT&search=&hits=80
| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM839nnn/GSM839364/suppl/GSM839364.CEL.gz
| Sample_series_id | GSE33950
| Sample_data_row_count | 54675
| |
|
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