Search results for the GEO ID: GSE39890  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM980760 | GPL570 |
|
KGN Control [RR1003]
|
KGN
|
cell line: KGN
transfection: GC matched control
|
|
| Sample_geo_accession | GSM980760
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980760/suppl/GSM980760_RR1003_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980761 | GPL570 |
|
KGN Knockdown [RR1004]
|
KGN
|
cell line: KGN
transfection: FOXL2 stealth RNAi
|
|
| Sample_geo_accession | GSM980761
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980761/suppl/GSM980761_RR1004_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980762 | GPL570 |
|
KGN Control [RR1006]
|
KGN
|
cell line: KGN
transfection: GC matched control
|
|
| Sample_geo_accession | GSM980762
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980762/suppl/GSM980762_RR1006_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980763 | GPL570 |
|
KGN Knockdown [RR1007]
|
KGN
|
cell line: KGN
transfection: FOXL2 stealth RNAi
|
|
| Sample_geo_accession | GSM980763
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980763/suppl/GSM980763_RR1007_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980764 | GPL570 |
|
KGN Knockdown [RR1008]
|
KGN
|
cell line: KGN
transfection: FOXL2 stealth RNAi
|
|
| Sample_geo_accession | GSM980764
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980764/suppl/GSM980764_RR1008_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980765 | GPL570 |
|
KGN Control [RR1009]
|
KGN
|
cell line: KGN
transfection: GC matched control
|
|
| Sample_geo_accession | GSM980765
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980765/suppl/GSM980765_RR1009_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980766 | GPL570 |
|
COV434 Control [RR1016]
|
COV434
|
cell line: COV434
transfection: empty vector
|
|
| Sample_geo_accession | GSM980766
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980766/suppl/GSM980766_RR1016_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980767 | GPL570 |
|
COV434 Mutant [RR1017]
|
COV434
|
cell line: COV434
transfection: pFOXL2m
|
|
| Sample_geo_accession | GSM980767
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980767/suppl/GSM980767_RR1017_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980768 | GPL570 |
|
COV434 Wildtype [RR1018]
|
COV434
|
cell line: COV434
transfection: pFOXL2wt
|
|
| Sample_geo_accession | GSM980768
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980768/suppl/GSM980768_RR1018_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980769 | GPL570 |
|
COV434 Mutant [RR1019]
|
COV434
|
cell line: COV434
transfection: Mutant
|
|
| Sample_geo_accession | GSM980769
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980769/suppl/GSM980769_RR1019_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980770 | GPL570 |
|
COV434 Wildtype [RR1020]
|
COV434
|
cell line: COV434
transfection: pFOXL2wt
|
|
| Sample_geo_accession | GSM980770
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980770/suppl/GSM980770_RR1020_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980771 | GPL570 |
|
COV434 Control [RR1021]
|
COV434
|
cell line: COV434
transfection: empty vector
|
|
| Sample_geo_accession | GSM980771
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980771/suppl/GSM980771_RR1021_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980772 | GPL570 |
|
COV434 Wildtype [RR1022]
|
COV434
|
cell line: COV434
transfection: pFOXL2wt
|
|
| Sample_geo_accession | GSM980772
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980772/suppl/GSM980772_RR1022_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980773 | GPL570 |
|
COV434 Control [RR1023]
|
COV434
|
cell line: COV434
transfection: empty vector
|
|
| Sample_geo_accession | GSM980773
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980773/suppl/GSM980773_RR1023_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
GSM980774 | GPL570 |
|
COV434 Mutant [RR1024]
|
COV434
|
cell line: COV434
transfection: pFOXL2m
|
|
| Sample_geo_accession | GSM980774
| | Sample_status | Public on Nov 05 2012
| | Sample_submission_date | Aug 06 2012
| | Sample_last_update_date | Nov 05 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | For siRNA knockdown of mutant FOXL2, KGN cells, passage 8, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with FOXL2 stealth RNAi™ (cat#HSS101080 Invitrogen, NZ) or a GC matched control using Lipofectamine 2000 and Opti-MEM serum free media (Invitrogen, NZ). RNAi-lipid complexes were removed 7h post transfection and replaced with complete media. For overexpression of wildtype or mutant FOXL2, COV434 cells, passage 9, were seeded at a density of 300,000 cells per well of a six well plate. Cells were transfected with 1µg of control (empty vector), pFOXL2wt, or pFOXL2m using Lipofectamine 2000 and Opti-MEM serum free media. Plasmid-lipid complexes were removed 7h post transfection and replaced with complete media.
| | Sample_growth_protocol_ch1 | Both cell lines were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 1% L-glutamine and 1% non essential amino acids, and maintained at 37°C in 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Cells were harvested 24h post transfection and total RNA was extracted using TRIzol® reagent (Ambion, NZ). Chloroform was added to the TRIzol® to separate the phases, and the aqueous phase was combined with 70% ethanol and passed through an RNeasy column (Qiagen, Australia) according to manufacturer’s instructions.
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | 105ng of total RNA from the knockdown and overexpression experiments was labelled using the MessageAmp™ Premier amplification according to manufacturer’s instructions (Ambion, NZ).
| | Sample_hyb_protocol | 8.5µg of labelled aRNA was hybridised to Affymetrix U133 Plus 2 microarrays.
| | Sample_scan_protocol | Affymetrix protocol
| | Sample_data_processing | RMA normalisation method
| | Sample_platform_id | GPL570
| | Sample_contact_name | Roseanne,,Rosario
| | Sample_contact_email | r.rosario@auckland.ac.nz
| | Sample_contact_institute | University of Auckland
| | Sample_contact_address | 85 Park Road, Grafton
| | Sample_contact_city | Auckland
| | Sample_contact_zip/postal_code | 1023
| | Sample_contact_country | New Zealand
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM980nnn/GSM980774/suppl/GSM980774_RR1024_HG-U133_Plus_2_.CEL.gz
| | Sample_series_id | GSE39890
| | Sample_data_row_count | 54675
| | |
|
| |
| |
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