Search results for the GEO ID: GSE34959  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM859567 | GPL1261 |
|
WT 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
|
CTL-1
|
| Sample_geo_accession | GSM859567
| | 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 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.
| | 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/GSM859567/suppl/GSM859567.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859568 | GPL1261 |
|
WT 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
|
CTL-2
|
| Sample_geo_accession | GSM859568
| | 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 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.
| | 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/GSM859568/suppl/GSM859568.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859569 | GPL1261 |
|
WT 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
|
CTL-3
|
| Sample_geo_accession | GSM859569
| | 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 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.
| | 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/GSM859569/suppl/GSM859569.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859570 | GPL1261 |
|
Ezh2-null 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
|
EZH2-1
|
| Sample_geo_accession | GSM859570
| | 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 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.
| | 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/GSM859570/suppl/GSM859570.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859571 | GPL1261 |
|
Ezh2-null 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
|
EZH2-2
|
| Sample_geo_accession | GSM859571
| | 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 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.
| | 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/GSM859571/suppl/GSM859571.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859572 | GPL1261 |
|
Ezh2-null 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
|
EZH2-3
|
| Sample_geo_accession | GSM859572
| | 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 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.
| | 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/GSM859572/suppl/GSM859572.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859573 | GPL1261 |
|
Ezh2-null 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
|
EZH2-4
|
| Sample_geo_accession | GSM859573
| | 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 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.
| | 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/GSM859573/suppl/GSM859573.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859574 | GPL1261 |
|
Eed-null MLL-AF9 BM-cells, biological rep1
|
Sorted GFP+/YFP+ bone marrow cells, Eed-null
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: Eed-null
cell type: sorted GFP+/YFP+ bone marrow cells
|
EED-1
|
| Sample_geo_accession | GSM859574
| | 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 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.
| | 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/GSM859574/suppl/GSM859574.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
| | |
|
GSM859575 | GPL1261 |
|
Eed-null MLL-AF9 BM-cells, biological rep2
|
Sorted GFP+/YFP+ bone marrow cells, Eed-null
|
background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: Eed-null
cell type: sorted GFP+/YFP+ bone marrow cells
|
EED-2
|
| Sample_geo_accession | GSM859575
| | 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 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.
| | 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/GSM859575/suppl/GSM859575.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
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GSM859576 | GPL1261 |
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Eed-null MLL-AF9 BM-cells, biological rep3
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Sorted GFP+/YFP+ bone marrow cells, Eed-null
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background strain: C57B/6
disease state: MLL-AF9-induced acute myeloid leukemia (AML)
genotype: Eed-null
cell type: sorted GFP+/YFP+ bone marrow cells
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EED-3
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| Sample_geo_accession | GSM859576
| | 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 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.
| | 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/GSM859576/suppl/GSM859576.CEL.gz
| | Sample_series_id | GSE34959
| | Sample_series_id | GSE34963
| | Sample_data_row_count | 45101
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