Search results for the GEO ID: GSE15646  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM391630 | GPL96 |
|
Kasumi-1_no_construct_no_transfection_rep1
|
Kasumi-1 AML cell line
|
construct: None
transfect method: None
sample scale factor: 0.5707874
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, no construct, no transfection, replicate 1
|
| Sample_geo_accession | GSM391630
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391630/suppl/GSM391630.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391631 | GPL96 |
|
Kasumi-1_no_construct_no_transfection_rep3
|
Kasumi-1 AML cell line
|
construct: None
transfect method: None
sample scale factor: 1
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, no construct, no transfection, replicate 3
|
| Sample_geo_accession | GSM391631
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391631/suppl/GSM391631.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391632 | GPL96 |
|
Kasumi-1_no_construct_Amaxa_nucleofection_transfection_rep1
|
Kasumi-1 AML cell line
|
construct: None
transfect method: Amaxa nucleofection
sample scale factor: 1.117535
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, no construct, Amaxa nucleofection transfection, replicate 1
|
| Sample_geo_accession | GSM391632
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391632/suppl/GSM391632.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391633 | GPL96 |
|
Kasumi-1_luciferase_construct_Biorad_siLentFect_transfection_rep1
|
Kasumi-1 AML cell line
|
construct: luciferase
transfect method: Biorad siLentFect
sample scale factor: 1.06261
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Biorad siLentFect transfection, replicate 1
|
| Sample_geo_accession | GSM391633
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391633/suppl/GSM391633.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391634 | GPL96 |
|
Kasumi-1_luciferase_construct_Biorad_siLentFect_transfection_rep2
|
Kasumi-1 AML cell line
|
construct: luciferase
transfect method: Biorad siLentFect
sample scale factor: 0.8701811
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Biorad siLentFect transfection, replicate 2
|
| Sample_geo_accession | GSM391634
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391634/suppl/GSM391634.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391635 | GPL96 |
|
Kasumi-1_luciferase_construct_Biorad_siLentFect_transfection_rep3
|
Kasumi-1 AML cell line
|
construct: luciferase
transfect method: Biorad siLentFect
sample scale factor: 0.62732816
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Biorad siLentFect transfection, replicate 3
|
| Sample_geo_accession | GSM391635
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391635/suppl/GSM391635.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391636 | GPL96 |
|
Kasumi-1_luciferase_construct_Amaxa_nucleofection_transfection_rep1
|
Kasumi-1 AML cell line
|
construct: luciferase
transfect method: Amaxa nucleofection
sample scale factor: 1.170961
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Amaxa nucleofection transfection, replicate 1
|
| Sample_geo_accession | GSM391636
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391636/suppl/GSM391636.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391637 | GPL96 |
|
Kasumi-1_luciferase_construct_Amaxa_nucleofection_transfection_rep2
|
Kasumi-1 AML cell line
|
construct: luciferase
transfect method: Amaxa nucleofection
sample scale factor: 1.5272099
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, luciferase construct, Amaxa nucleofection transfection, replicate 2
|
| Sample_geo_accession | GSM391637
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391637/suppl/GSM391637.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391638 | GPL96 |
|
Kasumi-1_AML1-ETO_construct_Biorad_siLentFect_transfection_rep1
|
Kasumi-1 AML cell line
|
construct: AML1-ETO
transfect method: Biorad siLentFect
sample scale factor: 0.8726512
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Biorad siLentFect transfection, replicate 1
|
| Sample_geo_accession | GSM391638
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391638/suppl/GSM391638.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391639 | GPL96 |
|
Kasumi-1_AML1-ETO_construct_Biorad_siLentFect_transfection_rep2
|
Kasumi-1 AML cell line
|
construct: AML1-ETO
transfect method: Biorad siLentFect
sample scale factor: 1.1518593
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Biorad siLentFect transfection, replicate 2
|
| Sample_geo_accession | GSM391639
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391639/suppl/GSM391639.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391640 | GPL96 |
|
Kasumi-1_AML1-ETO_construct_Biorad_siLentFect_transfection_rep3
|
Kasumi-1 AML cell line
|
construct: AML1-ETO
transfect method: Biorad siLentFect
sample scale factor: 0.48840404
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Biorad siLentFect transfection, replicate 3
|
| Sample_geo_accession | GSM391640
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391640/suppl/GSM391640.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391641 | GPL96 |
|
Kasumi-1_AML1-ETO_construct_Amaxa_nucleofection_transfection_rep1
|
Kasumi-1 AML cell line
|
construct: AML1-ETO
transfect method: Amaxa nucleofection
sample scale factor: 1.2448635
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Amaxa nucleofection transfection, replicate 1
|
| Sample_geo_accession | GSM391641
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391641/suppl/GSM391641.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
| | |
|
GSM391642 | GPL96 |
|
Kasumi-1_AML1-ETO_construct_Amaxa_nucleofection_transfection_rep2
|
Kasumi-1 AML cell line
|
construct: AML1-ETO
transfect method: Amaxa nucleofection
sample scale factor: 0.9635204
cell line: Kasumi-1
|
Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Amaxa nucleofection transfection, replicate 2
|
| Sample_geo_accession | GSM391642
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391642/suppl/GSM391642.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
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GSM391643 | GPL96 |
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Kasumi-1_AML1-ETO_construct_Amaxa_nucleofection_transfection_rep3
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Kasumi-1 AML cell line
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construct: AML1-ETO
transfect method: Amaxa nucleofection
sample scale factor: 1.5609292
cell line: Kasumi-1
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Gene expression data from Kasumi-1 at 96 hours, AML1-ETO construct, Amaxa nucleofection transfection, replicate 3
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| Sample_geo_accession | GSM391643
| | Sample_status | Public on May 01 2009
| | Sample_submission_date | Apr 13 2009
| | Sample_last_update_date | Apr 13 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The siRNA constructs against AML1-ETO and firefly luciferase were designed as previously described (Heidenreich O, Krauter J, Riehle H, et al. AML1/MTG8 oncogene suppression by small interfering RNAs supports myeloid differentiation of t(8;21)-positive leukemic cells. Blood. 2003;101:3157-3163.). The AML1-ETO-directed siRNA contained CCUCGAAAUCGUACUGAGAdTdT as the sense strand and UCUCAGUACGAUUUCGAGGdTdT as the antisense strand. The control firefly luciferase (siGL)-directed siRNA contained CGUACGCGGAAUACUUCGAdTdT as the sense strand and UCGAAGUAUUCGGCGUACGdTdT as the antisense strand. RNA sequences were synthesized by Dharmacon. Lyophilized siRNA was resuspended in 1x siRNA buffer (20 mM KCl, 6 mM HEPES pH 7.5, 0.02 mM MgCl2) and aliquoted for storage at a final concentration of 75 uM. Cells were transfected either by Amaxa nucleofection or by siLentFect lipid-based reagent (Biorad). Amaxa transfection was performed using 2 µl siRNA in 100 µl Amaxa buffer V (final siRNA concentration 1.5 uM) and program P-19 per the manufacturer’s protocol. For the cells transfected by lipid reagent, siRNA was diluted into serum-free medium at a final concentration of 240 nM and incubated with siLentFect (1.5 µl per 25 µl medium) for 20 minutes at room temperature before addition to 500,000 Kasumi-1 cells per well in 500 µl medium. Following transfection, cells were incubated at 37° C for 96 hours. Knockdown of AML1-ETO was confirmed by immunoblot and real-time PCR.
| | Sample_growth_protocol_ch1 | Cells were cultured in RPMI 1640 (Cellgro) with 10% fetal calf serum (FCS) (Sigma-Aldrich) and 1% penicillin-streptomycin.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA was extracted with TRIzol per the manufacturer’s guidelines, and 10 ug was used to create microarray target samples.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | First strand cDNA synthesis was generated using a T7-linked oligo-dT primer, followed by second strand synthesis. An in vitro transcription reaction was performed to generate cRNA containing biotinylated UTP and CTP, which was subsequently chemically fragmented at 95°C for 35 minutes.
| | Sample_hyb_protocol | Ten micrograms of the fragmented, biotinylated cRNA was hybridized in MES buffer (2-[N-Morpholino]ethansulfonic acid) containing 0.5 mg/ml acetylated bovine serum albumin (Sigma) to Affymetrix U133A arrays at 45°C for 16 hours.
| | Sample_scan_protocol | Scans were performed on Affymetrix scanners.
| | Sample_data_processing | The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix's default analysis settings. The samples in the data set have been scaled so that the mean expression of all genes for each sample is equal to the mean expression of all genes for the median sample.
| | Sample_platform_id | GPL96
| | Sample_contact_name | Kimberly,,Stegmaier
| | Sample_contact_email | kimberly_stegmaier@dfci.harvard.edu
| | Sample_contact_department | Department of Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute and Children’s Hospital Boston
| | Sample_contact_address | Harvard Medical School
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02115
| | Sample_contact_country | USA
| | Sample_contact_web_link | www.broad.mit.edu/cancer/
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM391nnn/GSM391643/suppl/GSM391643.CEL.gz
| | Sample_series_id | GSE15646
| | Sample_series_id | GSE15648
| | Sample_data_row_count | 22283
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