Search results for the GEO ID: GSE39902  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM981074 | GPL570 |
|
MII siGFP, biological replicate A
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with Control siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with Control siRNA
|
Gene expression data from control MII cells
|
| Sample_geo_accession | GSM981074
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981074/suppl/GSM981074_L17_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981075 | GPL570 |
|
MII siGFP, biological replicate B
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with Control siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with Control siRNA
|
Gene expression data from control MII cells
|
| Sample_geo_accession | GSM981075
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981075/suppl/GSM981075_L18_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981076 | GPL570 |
|
MII siGFP, biological replicate C
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with Control siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with Control siRNA
|
Gene expression data from control MII cells
|
| Sample_geo_accession | GSM981076
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981076/suppl/GSM981076_L19_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981077 | GPL570 |
|
MII siGFP, biological replicate D
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with Control siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with Control siRNA
|
Gene expression data from control MII cells
|
| Sample_geo_accession | GSM981077
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981077/suppl/GSM981077_L20_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981078 | GPL570 |
|
MII siAPC, biological replicate A
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with APC siRNA
|
Gene expression data from MII cells depleted of APC
|
| Sample_geo_accession | GSM981078
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981078/suppl/GSM981078_L25_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981079 | GPL570 |
|
MII siAPC, biological replicate B
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with APC siRNA
|
Gene expression data from MII cells depleted of APC
|
| Sample_geo_accession | GSM981079
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981079/suppl/GSM981079_L26_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981080 | GPL570 |
|
MII siAPC, biological replicate C
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with APC siRNA
|
Gene expression data from MII cells depleted of APC
|
| Sample_geo_accession | GSM981080
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981080/suppl/GSM981080_L27_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981081 | GPL570 |
|
MII siAPC, biological replicate D
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with APC siRNA
|
Gene expression data from MII cells depleted of APC
|
| Sample_geo_accession | GSM981081
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981081/suppl/GSM981081_L28_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981082 | GPL570 |
|
MII siAPC/siTAZ, biological replicate A
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA and TAZ siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with APC siRNA and TAZ siRNA
|
Gene expression data from MII cells depleted of APC and TAZ
|
| Sample_geo_accession | GSM981082
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981082/suppl/GSM981082_L29_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981083 | GPL570 |
|
MII siAPC/siTAZ, biological replicate B
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA and TAZ siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with APC siRNA and TAZ siRNA
|
Gene expression data from MII cells depleted of APC and TAZ
|
| Sample_geo_accession | GSM981083
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981083/suppl/GSM981083_L30_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981084 | GPL570 |
|
MII siAPC/siTAZ, biological replicate C
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA and TAZ siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with APC siRNA and TAZ siRNA
|
Gene expression data from MII cells depleted of APC and TAZ
|
| Sample_geo_accession | GSM981084
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981084/suppl/GSM981084_L31_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981085 | GPL570 |
|
MII siAPC/siTAZ, biological replicate D
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with APC siRNA and TAZ siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with APC siRNA and TAZ siRNA
|
Gene expression data from MII cells depleted of APC and TAZ
|
| Sample_geo_accession | GSM981085
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981085/suppl/GSM981085_L32_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981086 | GPL570 |
|
MII sibcat, biological replicate A
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with beta-catenin siRNA
|
Gene expression data from MII cells depleted of b-catenin
|
| Sample_geo_accession | GSM981086
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981086/suppl/GSM981086_L33_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981087 | GPL570 |
|
MII sibcat, biological replicate B
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with beta-catenin siRNA
|
Gene expression data from MII cells depleted of b-catenin
|
| Sample_geo_accession | GSM981087
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981087/suppl/GSM981087_L34_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981088 | GPL570 |
|
MII sibcat, biological replicate C
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with beta-catenin siRNA
|
Gene expression data from MII cells depleted of b-catenin
|
| Sample_geo_accession | GSM981088
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981088/suppl/GSM981088_L35_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981089 | GPL570 |
|
MII sibcat, biological replicate D
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with beta-catenin siRNA
|
Gene expression data from MII cells depleted of b-catenin
|
| Sample_geo_accession | GSM981089
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981089/suppl/GSM981089_L36_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981090 | GPL570 |
|
MII sibcat/siTAZ, biological replicate A
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA and TAZ siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with beta-catenin siRNA and TAZ siRNA
|
Gene expression data from MII cells depleted of b-catenin and TAZ
|
| Sample_geo_accession | GSM981090
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981090/suppl/GSM981090_L37_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981091 | GPL570 |
|
MII sibcat/siTAZ, biological replicate B
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA and TAZ siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with beta-catenin siRNA and TAZ siRNA
|
Gene expression data from MII cells depleted of b-catenin and TAZ
|
| Sample_geo_accession | GSM981091
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981091/suppl/GSM981091_L38_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981092 | GPL570 |
|
MII sibcat/siTAZ, biological replicate C
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA and TAZ siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with beta-catenin siRNA and TAZ siRNA
|
Gene expression data from MII cells depleted of b-catenin and TAZ
|
| Sample_geo_accession | GSM981092
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981092/suppl/GSM981092_L39_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
|
GSM981093 | GPL570 |
|
MII sibcat/siTAZ, biological replicate D
|
human mammary epithelial cell line (RAS-transformed) MCF10-T1k (MII), transfected with beta-catenin siRNA and TAZ siRNA
|
cell line: MCF10-T1k (MII)
treatment: transfected with beta-catenin siRNA and TAZ siRNA
|
Gene expression data from MII cells depleted of b-catenin and TAZ
|
| Sample_geo_accession | GSM981093
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Dec 21 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Cells were transfected with siRNA by using RNAi MAX (Life Technologies), following manifacturer's instructions
| | Sample_growth_protocol_ch1 | MII cells were cultured in DMEM/F12 (Gibco, Life Technologies) with 5% HS, glutamine and antibiotics, freshly supplemented with insulin, EGF, hydrocortisone, and cholera toxin.
| | 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/GSM981nnn/GSM981093/suppl/GSM981093_L40_P_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39902
| | Sample_series_id | GSE39907
| | Sample_data_row_count | 54675
| | |
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