Search results for the GEO ID: GSE34961  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM859583 | GPL1261 |
|
WT 2'MLL-AF9 BM-Cells, biological rep1
|
Sorted GFP+/YFP+ bone marrow cells, WT
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: WT
cell type: sorted GFP+/YFP+ bone marrow cells
|
2CTL-1
|
| Sample_geo_accession | GSM859583
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859583/suppl/GSM859583.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859584 | GPL1261 |
|
WT 2'MLL-AF9 BM-Cells, biological rep2
|
Sorted GFP+/YFP+ bone marrow cells, WT
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: WT
cell type: sorted GFP+/YFP+ bone marrow cells
|
2CTL-2
|
| Sample_geo_accession | GSM859584
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859584/suppl/GSM859584.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859585 | GPL1261 |
|
WT 2'MLL-AF9 BM-Cells, biological rep3
|
Sorted GFP+/YFP+ bone marrow cells, WT
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: WT
cell type: sorted GFP+/YFP+ bone marrow cells
|
2CTL-3
|
| Sample_geo_accession | GSM859585
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859585/suppl/GSM859585.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859586 | GPL1261 |
|
WT 2'MLL-AF9 BM-Cells, biological rep4
|
Sorted GFP+/YFP+ bone marrow cells, WT
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: WT
cell type: sorted GFP+/YFP+ bone marrow cells
|
2CTL-4
|
| Sample_geo_accession | GSM859586
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859586/suppl/GSM859586.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859587 | GPL1261 |
|
Ezh2-null 2'MLL-AF9 BM-Cells, biological rep1
|
Sorted GFP+/YFP+ bone marrow cells, Ezh2-null
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: Ezh2-null
cell type: sorted GFP+/YFP+ bone marrow cells
|
2EZH2-1
|
| Sample_geo_accession | GSM859587
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859587/suppl/GSM859587.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859588 | GPL1261 |
|
Ezh2-null 2'MLL-AF9 BM-Cells, biological rep2
|
Sorted GFP+/YFP+ bone marrow cells, Ezh2-null
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: Ezh2-null
cell type: sorted GFP+/YFP+ bone marrow cells
|
2EZH2-2
|
| Sample_geo_accession | GSM859588
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859588/suppl/GSM859588.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859589 | GPL1261 |
|
Ezh2-null 2'MLL-AF9 BM-Cells, biological rep3
|
Sorted GFP+/YFP+ bone marrow cells, Ezh2-null
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: Ezh2-null
cell type: sorted GFP+/YFP+ bone marrow cells
|
2EZH2-3
|
| Sample_geo_accession | GSM859589
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859589/suppl/GSM859589.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859590 | GPL1261 |
|
Ezh2-null 2'MLL-AF9 BM-Cells, biological rep4
|
Sorted GFP+/YFP+ bone marrow cells, Ezh2-null
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: Ezh2-null
cell type: sorted GFP+/YFP+ bone marrow cells
|
2EZH2-4
|
| Sample_geo_accession | GSM859590
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859590/suppl/GSM859590.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859591 | GPL1261 |
|
Ezh2-null 2'MLL-AF9 BM-Cells, biological rep5
|
Sorted GFP+/YFP+ bone marrow cells, Ezh2-null
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: Ezh2-null
cell type: sorted GFP+/YFP+ bone marrow cells
|
2EZH2-5
|
| Sample_geo_accession | GSM859591
| | Sample_status | Public on Feb 22 2012
| | Sample_submission_date | Jan 09 2012
| | Sample_last_update_date | Feb 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Bone marrow cells from secondary recipient leukemic mice were sorted based on Forward/Side Scatter, Propidium Iodide negativity and GFP/YFP double positivity. GFP indicates retroviral gene transfer of MLL-AF9-ires-GFP, and YFP indicates successful Cre activation.
| | Sample_growth_protocol_ch1 | Leukemia was generated by injecting sublethally irradiated (600cGy) C57B/6 recipient mice with 100,000 cells from replated leukemic colonies and administering pIpC 2-3 weeks after transplantation after to activate Cre expression. Sorted GFP/YFP positive bone marrow cells were injected into sublethally (600cGy) irradiated secondary recipients.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | Total RNA was extracted using Trizol reagent. RNA was amplified using the NuGEN Ovation Pico WTA system (NuGEN, San Carlos, CA).
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | Amplified cDNA was labeled using the NuGEN Encore Biotin Module.
| | Sample_hyb_protocol | 5 mcg of amplified, labeled cDNA was hybridized to the Affymetrix 430 2.0 microarray using standard conditions.
| | Sample_scan_protocol | GeneChip Scanner 3000, 7G. Standard Affymetrix protocol.
| | Sample_data_processing | RMA background correction and quantile normalization was done with the GenePattern ExpressionFileCreator module (http://www.broad.mit.edu/cancer/software/genepattern/), which uses the Bioconductor implementation of RMA (http://www.bioconductor.org/). This function computes the Robust Multichip Average expression measure described in Irizarry et al. Biostatistics (2003).
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Amit,,Sinha
| | Sample_contact_email | amit.sinha@childrens.harvard.edu
| | Sample_contact_phone | 617-582-7579
| | Sample_contact_laboratory | Armstrong Lab
| | Sample_contact_department | Pediatric Oncology
| | Sample_contact_institute | Dana-Farber Cancer Institute
| | Sample_contact_address | 44 Binney St
| | Sample_contact_city | Boston
| | Sample_contact_state | MA
| | Sample_contact_zip/postal_code | 02135
| | Sample_contact_country | USA
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM859nnn/GSM859591/suppl/GSM859591.CEL.gz
| | Sample_series_id | GSE34961
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
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Make groups for comparisons |
(2 groups will be compared at a time) |
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| Select GSMs and click on "Add groups" |
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