Search results for the GEO ID: GSE46362  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1129184 | GPL570 |
|
Overexpression of scrambled miR-control in stable miR-125b-expressing Reh cells, rep1
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus scrambled miR-control
|
|
| Sample_geo_accession | GSM1129184
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129184/suppl/GSM1129184_KGK_Ball_ET_combi5.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129185 | GPL570 |
|
Overexpression of scrambled miR-control in stable miR-125b-expressing Reh cells, rep2
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus scrambled miR-control
|
|
| Sample_geo_accession | GSM1129185
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129185/suppl/GSM1129185_KGK_Ball_ET_combi6.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129186 | GPL570 |
|
Overexpression of miR-99a in stable miR-125b-expressing Reh cells, rep1
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-99a
|
|
| Sample_geo_accession | GSM1129186
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129186/suppl/GSM1129186_KGK_Ball_ET_combi7.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129187 | GPL570 |
|
Overexpression of miR-99a in stable miR-125b-expressing Reh cells, rep2
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-99a
|
|
| Sample_geo_accession | GSM1129187
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129187/suppl/GSM1129187_KGK_Ball_ET_combi8.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129188 | GPL570 |
|
Overexpression of miR-99a in stable miR-125b-expressing Reh cells, rep3
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-99a
|
|
| Sample_geo_accession | GSM1129188
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129188/suppl/GSM1129188_KGK_Ball_ET_combi9.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129189 | GPL570 |
|
Overexpression of miR-100 in stable miR-125b-expressing Reh cells, rep1
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-100
|
|
| Sample_geo_accession | GSM1129189
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129189/suppl/GSM1129189_KGK_Ball_ET_combi10.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129190 | GPL570 |
|
Overexpression of miR-100 in stable miR-125b-expressing Reh cells, rep2
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-100
|
|
| Sample_geo_accession | GSM1129190
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129190/suppl/GSM1129190_KGK_Ball_ET_combi11.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129191 | GPL570 |
|
Overexpression of miR-100 in stable miR-125b-expressing Reh cells, rep3
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-100
|
|
| Sample_geo_accession | GSM1129191
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129191/suppl/GSM1129191_KGK_Ball_ET_combi12.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129192 | GPL570 |
|
Overexpression of miR-99a and miR-100 in stable miR-125b-expressing Reh cells, rep1
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-99a and miR-100
|
|
| Sample_geo_accession | GSM1129192
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129192/suppl/GSM1129192_KGK_Ball_ET_combi13_2.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129193 | GPL570 |
|
Overexpression of miR-99a and miR-100 in stable miR-125b-expressing Reh cells, rep2
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-99a and miR-100
|
|
| Sample_geo_accession | GSM1129193
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129193/suppl/GSM1129193_KGK_Ball_ET_combi14.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
|
GSM1129194 | GPL570 |
|
Overexpression of miR-99a and miR-100 in stable miR-125b-expressing Reh cells, rep3
|
ETV6-RUNX1-positive Reh leukemic cells
|
cell line: Reh
sample type: overexpressing miR-125b plus miR-99a and miR-100
|
|
| Sample_geo_accession | GSM1129194
| | Sample_status | Public on Jun 27 2013
| | Sample_submission_date | Apr 24 2013
| | Sample_last_update_date | Jun 27 2013
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Homo sapiens
| | Sample_taxid_ch1 | 9606
| | Sample_treatment_protocol_ch1 | The ETV6-RUNX1-positive leukemic cell line Reh was spin-infected by adding virus particles at a multiplicity of infection (MOI) of 2.5 TU/cell and 5 μg/mL polybrene . After 48 hours, the infection rate was determined by measuring eGFP positivity by flow cytometry. Stably expressing miR-125b and scrambled miR-control cell lines were generated by culturing cells for at least two weeks. In the presence of Lipofectamine, 66 µM precursor oligonucleotide sequences for miR-125b, miR-99a, miR-100 or scrambled control miR #1 to stably miR-125b-expressing Reh cells. After 72 hours, new precursor oligos were added to the cells. Similarly, the combination of miR-99a and miR-100 was used for transfection and we used half amount (33 µM) of each miRNA to keep different experimental conditions comparable. Cells were harvested 48 hours after the second transfection, for further analysis.
| | Sample_growth_protocol_ch1 | Reh cells (0.8x106/mL) were incubated in triplicate at 37°C in humidified air with 5% CO2.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Trizol extraction of total RNA was performed according to the manufacturer's instructions.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | The Affymetrix One-Cycle cDNA Synthesis kit and the GeneChip IVT Labeling kit (Santa Clara, CA, USA) were used to synthesize cRNA, according to the manufacturer's instructions.
| | Sample_hyb_protocol | Following fragmentation, 11 ug of cRNA were hybridized for 16 hr at 45C @60 RPM. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
| | Sample_scan_protocol | GeneChips were scanned using the 7G Affymetrix GeneChip Scanner.
| | Sample_data_processing | The data were preprocessed using vsnrma in R2.14.1 using the affy1.32.1 and vsn3.22.0 Bioconductor2.14.0 packages.
| | Sample_platform_id | GPL570
| | Sample_contact_name | Farhad,,Akbari Moqadam
| | Sample_contact_email | farhad.moqadam@gmail.com
| | Sample_contact_phone | 107043891
| | Sample_contact_institute | ErasmusMC - department of biostatistics
| | Sample_contact_address | dr. Molewaterplein 50
| | Sample_contact_city | Rotterdam
| | Sample_contact_state = N/A | Not Applicable
| | Sample_contact_zip/postal_code | 3015 GE
| | Sample_contact_country | Netherlands
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1129nnn/GSM1129194/suppl/GSM1129194_KGK_Ball_ET_combi15.CEL.gz
| | Sample_series_id | GSE46362
| | Sample_data_row_count | 54675
| | |
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