Search results for the GEO ID: GSE14964  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM373614 | GPL570 |
|
Vector control 1
|
HeLa cells transduced LKO control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373614
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373614/suppl/GSM373614.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373614/suppl/GSM373614.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373615 | GPL570 |
|
Vector control 2
|
HeLa cells transduced LKO control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373615
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373615/suppl/GSM373615.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373615/suppl/GSM373615.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373616 | GPL570 |
|
Vector control 3
|
HeLa cells transduced LKO control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373616
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373616/suppl/GSM373616.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373616/suppl/GSM373616.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373617 | GPL570 |
|
First shYY1
|
HeLa cells transduced shYY1 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373617
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373617/suppl/GSM373617.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373617/suppl/GSM373617.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373618 | GPL570 |
|
Second shYY1
|
HeLa cells transduced shYY1 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373618
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373618/suppl/GSM373618.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373618/suppl/GSM373618.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373619 | GPL570 |
|
Third shYY1
|
HeLa cells transduced shYY1 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373619
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373619/suppl/GSM373619.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373619/suppl/GSM373619.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373620 | GPL570 |
|
First shYY2
|
HeLa cells transduced shYY2 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373620
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373620/suppl/GSM373620.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373620/suppl/GSM373620.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373621 | GPL570 |
|
Second shYY2
|
HeLa cells transduced shYY2 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373621
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373621/suppl/GSM373621.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373621/suppl/GSM373621.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373622 | GPL570 |
|
Third shYY2
|
HeLa cells transduced shYY2 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373622
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373622/suppl/GSM373622.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373622/suppl/GSM373622.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373623 | GPL570 |
|
Fourth shYY2
|
HeLa cells transduced shYY2 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373623
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373623/suppl/GSM373623.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373623/suppl/GSM373623.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373624 | GPL570 |
|
First shYY1 and shYY2
|
HeLa cells transduced shYY1shYY2 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373624
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373624/suppl/GSM373624.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373624/suppl/GSM373624.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373625 | GPL570 |
|
Second shYY1 and shYY2
|
HeLa cells transduced shYY1shYY2 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373625
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373625/suppl/GSM373625.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373625/suppl/GSM373625.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
GSM373626 | GPL570 |
|
Third shYY1 and shYY2
|
HeLa cells transduced shYY1shYY2 control lentivirus.
|
cell line: HeLa
|
n/a
|
| Sample_geo_accession | GSM373626
| | Sample_status | Public on Feb 28 2010
| | Sample_submission_date | Feb 24 2009
| | Sample_last_update_date | Dec 22 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | Lentiviral pLKO-shRNAs were obtained from Sigma-Aldrich. The tracking numbers of the most effective shRNAs are TRCN0000019894 (YY1), TRCN0000016494 (YY2). To replace the puromycin-resistance gene in pLKO plasmids by neomycin-resistance for combined knockdown, an 827 bp fragment containing neoR gene was amplified from plasmid pCNH with primers 5'-TCA GGA TCC AGG ATC GTT TCG CAT GAT TGA AC-3' and 5'-TCA GGT ACC GAT GCA TGA GTC CCG CTC AGA AGA ACT CG-3', digested by Kpn I and BamH I, and ligated to Kpn I/BamH I-treated pLKO- shRNA plasmids. pLKO-shRNAs were packaged in 293T cells following the manufacturer’s standard protocol (Sigma-Aldrich). Spent medium of 293T cells was collected at 24-hour and 48-hour post-transfection, pooled, and cleared through a 0.45-micron syringe filter. To in-fect, HeLa cells were grown in 6-well culture plates in 2 ml medium and 0.5 ml of lenti-virus-containing medium was added. After 72 hours, cells were selected and maintained in medium containing 2 mg/ml of puromycin. To make combined shRNA transfectants, this process was repeated but selected using 500 mg/ml of Geneticin G418 for dual se-lections. Stable transfectants were split once a week and cells of less than fifteen pas-sages were used in all assays.
| | Sample_growth_protocol_ch1 | HeLa cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum, and maintained in 37°C incubators with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was prepared by Trizol Reagent (Invitrogen). Ten micrograms of RNA were used to hybridize the Affymetrix U133A2.0 human genome array.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix One-Cycle Target Labeling and Control Reagents (Part#900493) + Enzo BioArray High Yield RNA Transcript Labelling Kit (Part#42655)
| | Sample_hyb_protocol = Microarray | Affymetrix GeneChip Human Genome U133 Plus 2.0. Affymetrix Hybridization Oven= 645. Affymetrix Fluidics Station= 450. Fluidics Protocol= EukGE-WS2
| | Sample_scan_protocol | Affymetrix GeneChip Scanner= 3000-7G. Controller= GCOS
| | Sample_data_processing | GCOS MAS 5
| | Sample_platform_id | GPL570
| | Sample_contact_name | Emmett,Vance,Schmidt
| | Sample_contact_email | schmidt@helix.mgh.harvard.edu
| | Sample_contact_phone | 617-726-5707
| | Sample_contact_fax | 617-726-8623
| | Sample_contact_laboratory | Jackson 9 - Oncology Floor
| | Sample_contact_department | Tumor Biology
| | Sample_contact_institute | Cancer Research Center at MGH
| | Sample_contact_address | 55 Fruit St. - GRJ904
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02114
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373626/suppl/GSM373626.CEL.gz
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM373nnn/GSM373626/suppl/GSM373626.CHP.gz
| | Sample_series_id | GSE14964
| | Sample_data_row_count | 54675
| | |
|
| |
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