Search results for the GEO ID: GSE20390  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM510625 | GPL1261 |
|
Control - repeat 1 - mAdbID:101315
|
Control
|
strain: BALB/c
tissue: colon
cell line: CT26
cell type: murine colon carcinoma
transfection: empty pU6-m3 vector
|
The empty pU6-m3 vector was transfected into the cells as described elsewhere (11, 12).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101315
|
| Sample_geo_accession | GSM510625
| | Sample_status | Public on Jul 07 2010
| | Sample_submission_date | Feb 17 2010
| | Sample_last_update_date | Jul 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol Extraction Protocol
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cells using TRIzol® Reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix Labeling Protocol
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Affymetrix Hybridization Protocol
| | Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 430.
| | Sample_scan_protocol | Affymetrix Scanning Protocol
| | Sample_scan_protocol | The Scanner 3000 was used to scan the microarrays.
| | Sample_data_processing | Affymetrix RMA Data Processing
| | Sample_data_processing | Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Petra,,Tsuji
| | Sample_contact_email | tsujipa@mail.nih.gov
| | Sample_contact_phone | 301-594-9930
| | Sample_contact_department | MBSS/LCP
| | Sample_contact_institute | NIH/NCI
| | Sample_contact_address | 37 Convent Dr
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510625/suppl/GSM510625.CEL.gz
| | Sample_series_id | GSE20390
| | Sample_data_row_count | 45101
| | |
|
GSM510626 | GPL1261 |
|
Control - repeat 2 - mAdbID:101316
|
Control
|
strain: BALB/c
tissue: colon
cell line: CT26
cell type: murine colon carcinoma
transfection: empty pU6-m3 vector
|
The empty pU6-m3 vector was transfected into the cells as described elsewhere (11, 12).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101316
|
| Sample_geo_accession | GSM510626
| | Sample_status | Public on Jul 07 2010
| | Sample_submission_date | Feb 17 2010
| | Sample_last_update_date | Jul 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol Extraction Protocol
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cells using TRIzol® Reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix Labeling Protocol
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Affymetrix Hybridization Protocol
| | Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 430.
| | Sample_scan_protocol | Affymetrix Scanning Protocol
| | Sample_scan_protocol | The Scanner 3000 was used to scan the microarrays.
| | Sample_data_processing | Affymetrix RMA Data Processing
| | Sample_data_processing | Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Petra,,Tsuji
| | Sample_contact_email | tsujipa@mail.nih.gov
| | Sample_contact_phone | 301-594-9930
| | Sample_contact_department | MBSS/LCP
| | Sample_contact_institute | NIH/NCI
| | Sample_contact_address | 37 Convent Dr
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510626/suppl/GSM510626.CEL.gz
| | Sample_series_id | GSE20390
| | Sample_data_row_count | 45101
| | |
|
GSM510627 | GPL1261 |
|
Control - repeat 3 - mAdbID:101317
|
Control
|
strain: BALB/c
tissue: colon
cell line: CT26
cell type: murine colon carcinoma
transfection: empty pU6-m3 vector
|
The empty pU6-m3 vector was transfected into the cells as described elsewhere (11, 12).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101317
|
| Sample_geo_accession | GSM510627
| | Sample_status | Public on Jul 07 2010
| | Sample_submission_date | Feb 17 2010
| | Sample_last_update_date | Jul 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol Extraction Protocol
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cells using TRIzol® Reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix Labeling Protocol
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Affymetrix Hybridization Protocol
| | Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 430.
| | Sample_scan_protocol | Affymetrix Scanning Protocol
| | Sample_scan_protocol | The Scanner 3000 was used to scan the microarrays.
| | Sample_data_processing | Affymetrix RMA Data Processing
| | Sample_data_processing | Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Petra,,Tsuji
| | Sample_contact_email | tsujipa@mail.nih.gov
| | Sample_contact_phone | 301-594-9930
| | Sample_contact_department | MBSS/LCP
| | Sample_contact_institute | NIH/NCI
| | Sample_contact_address | 37 Convent Dr
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510627/suppl/GSM510627.CEL.gz
| | Sample_series_id | GSE20390
| | Sample_data_row_count | 45101
| | |
|
GSM510628 | GPL1261 |
|
shSep15 - repeat 1 - mAdbID:101321
|
shSep15
|
strain: BALB/c
tissue: colon
cell line: CT26
cell type: murine colon carcinoma
transfection: pU6-m3 vector used for generating shRNA targets. To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3.
|
targeted down-regulation
The pU6-m3 vector used for generating shRNA targets was constructed as described elsewhere (11, 12). To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3 as previously described (11).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101321
|
| Sample_geo_accession | GSM510628
| | Sample_status | Public on Jul 07 2010
| | Sample_submission_date | Feb 17 2010
| | Sample_last_update_date | Jul 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol Extraction Protocol
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cells using TRIzol® Reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix Labeling Protocol
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Affymetrix Hybridization Protocol
| | Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 430.
| | Sample_scan_protocol | Affymetrix Scanning Protocol
| | Sample_scan_protocol | The Scanner 3000 was used to scan the microarrays.
| | Sample_data_processing | Affymetrix RMA Data Processing
| | Sample_data_processing | Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Petra,,Tsuji
| | Sample_contact_email | tsujipa@mail.nih.gov
| | Sample_contact_phone | 301-594-9930
| | Sample_contact_department | MBSS/LCP
| | Sample_contact_institute | NIH/NCI
| | Sample_contact_address | 37 Convent Dr
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510628/suppl/GSM510628.CEL.gz
| | Sample_series_id | GSE20390
| | Sample_data_row_count | 45101
| | |
|
GSM510629 | GPL1261 |
|
shSep15 - repeat 2 - mAdbID:101322
|
shSep15
|
strain: BALB/c
tissue: colon
cell line: CT26
cell type: murine colon carcinoma
transfection: pU6-m3 vector used for generating shRNA targets. To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3.
|
targeted down-regulation
The pU6-m3 vector used for generating shRNA targets was constructed as described elsewhere (11, 12). To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3 as previously described (11).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101322
|
| Sample_geo_accession | GSM510629
| | Sample_status | Public on Jul 07 2010
| | Sample_submission_date | Feb 17 2010
| | Sample_last_update_date | Jul 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol Extraction Protocol
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cells using TRIzol® Reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix Labeling Protocol
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Affymetrix Hybridization Protocol
| | Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 430.
| | Sample_scan_protocol | Affymetrix Scanning Protocol
| | Sample_scan_protocol | The Scanner 3000 was used to scan the microarrays.
| | Sample_data_processing | Affymetrix RMA Data Processing
| | Sample_data_processing | Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Petra,,Tsuji
| | Sample_contact_email | tsujipa@mail.nih.gov
| | Sample_contact_phone | 301-594-9930
| | Sample_contact_department | MBSS/LCP
| | Sample_contact_institute | NIH/NCI
| | Sample_contact_address | 37 Convent Dr
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510629/suppl/GSM510629.CEL.gz
| | Sample_series_id | GSE20390
| | Sample_data_row_count | 45101
| | |
|
GSM510630 | GPL1261 |
|
shSep15 - repeat 3 - mAdbID:101323
|
shSep15
|
strain: BALB/c
tissue: colon
cell line: CT26
cell type: murine colon carcinoma
transfection: pU6-m3 vector used for generating shRNA targets. To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3.
|
targeted down-regulation
The pU6-m3 vector used for generating shRNA targets was constructed as described elsewhere (11, 12). To knockdown Sep15 expression, 19-nt sequence 5’-acagaagagttccatttaa-3’ was chosen from the mouse Sep15 cDNA, which was unique to this gene. This sequence was annealed and inserted into the BamHI-HindIII cloning sites in pU6-m3 as previously described (11).
11. Yoo MH, Xu XM, Carlson BA, Gladyshev VN, Hatfield DL. Thioredoxin reductase 1 deficiency reverses tumor phenotypes and tumorigenicity of lung carcinoma cells J Biol Chem 2006;281:13005-13008.
12. Xu, X. M., Mix, H., Carlson, B. A., Grabowski, P. J., Gladyshev, V. N., Berry, M. J., and Hatfield, D. L. Evidence for direct roles of two additional factors, SECp43 and soluble liver antigen, in the selenoprotein synthesis machinery, J. Biol. Chem. 2005: 280, 41568-41575.
mAdb experiment ID: 101323
|
| Sample_geo_accession | GSM510630
| | Sample_status | Public on Jul 07 2010
| | Sample_submission_date | Feb 17 2010
| | Sample_last_update_date | Jul 07 2010
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol Extraction Protocol
| | Sample_extract_protocol_ch1 | Total RNA was extracted from cells using TRIzol® Reagent according to manufacturer's instructions (Invitrogen, Carlsbad, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Affymetrix Labeling Protocol
| | Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 1 microg total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).
| | Sample_hyb_protocol | Affymetrix Hybridization Protocol
| | Sample_hyb_protocol | Following fragmentation, 10 micrograms of cRNA were hybridized for 16 hours at 45C on U133 plus 2.0 arrays from Affymetrix. Arrays were washed and stained in the Affymetrix Fluidics Station 430.
| | Sample_scan_protocol | Affymetrix Scanning Protocol
| | Sample_scan_protocol | The Scanner 3000 was used to scan the microarrays.
| | Sample_data_processing | Affymetrix RMA Data Processing
| | Sample_data_processing | Calculation Method: Expression summary values were calculated using the Bioconductor implemented version of RMA (Robust Multichip Average).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Petra,,Tsuji
| | Sample_contact_email | tsujipa@mail.nih.gov
| | Sample_contact_phone | 301-594-9930
| | Sample_contact_department | MBSS/LCP
| | Sample_contact_institute | NIH/NCI
| | Sample_contact_address | 37 Convent Dr
| | Sample_contact_city | Bethesda
| | Sample_contact_state | MD
| | Sample_contact_zip/postal_code | 20892
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM510nnn/GSM510630/suppl/GSM510630.CEL.gz
| | Sample_series_id | GSE20390
| | Sample_data_row_count | 45101
| | |
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