Search results for the GEO ID: GSE40939  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM1005403 | GPL1261 |
|
control rep1
|
sorted GFP-positive cells
|
strain background: C57BL/6
cell source: bone marrow cells
cell population: Lineage-depleted c-Kit+ Lin– cells
transduction: MSCV-IRES-GFP-empty
|
SAMPLE 1
Gene expression data from murine hematopoietic stem and progenitor cells
|
| Sample_geo_accession | GSM1005403
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005403/suppl/GSM1005403_UB_mouse1.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005404 | GPL1261 |
|
control rep2
|
sorted GFP-positive cells
|
strain background: C57BL/6
cell source: bone marrow cells
cell population: Lineage-depleted c-Kit+ Lin– cells
transduction: MSCV-IRES-GFP-empty
|
SAMPLE 2
Gene expression data from murine hematopoietic stem and progenitor cells
|
| Sample_geo_accession | GSM1005404
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005404/suppl/GSM1005404_UB_mouse2.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005405 | GPL1261 |
|
control rep3
|
sorted GFP-positive cells
|
strain background: C57BL/6
cell source: bone marrow cells
cell population: Lineage-depleted c-Kit+ Lin– cells
transduction: MSCV-IRES-GFP-empty
|
SAMPLE 3
Gene expression data from murine hematopoietic stem and progenitor cells
|
| Sample_geo_accession | GSM1005405
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005405/suppl/GSM1005405_UB_mouse3.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005406 | GPL1261 |
|
murine Cdx2 rep1
|
sorted GFP-positive cells
|
strain background: C57BL/6
cell source: bone marrow cells
cell population: Lineage-depleted c-Kit+ Lin– cells
transduction: MSCV-IRES-GFP-mCdx2
|
SAMPLE 4
Gene expression data from murine hematopoietic stem and progenitor cells
|
| Sample_geo_accession | GSM1005406
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005406/suppl/GSM1005406_UB_mouse4_CDX2.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005407 | GPL1261 |
|
murine Cdx2 rep2
|
sorted GFP-positive cells
|
strain background: C57BL/6
cell source: bone marrow cells
cell population: Lineage-depleted c-Kit+ Lin– cells
transduction: MSCV-IRES-GFP-mCdx2
|
SAMPLE 5
Gene expression data from murine hematopoietic stem and progenitor cells
|
| Sample_geo_accession | GSM1005407
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005407/suppl/GSM1005407_UB_mouse5_CDX2.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005408 | GPL1261 |
|
murine Cdx2 rep3
|
sorted GFP-positive cells
|
strain background: C57BL/6
cell source: bone marrow cells
cell population: Lineage-depleted c-Kit+ Lin– cells
transduction: MSCV-IRES-GFP-mCdx2
|
SAMPLE 6
Gene expression data from murine hematopoietic stem and progenitor cells
|
| Sample_geo_accession | GSM1005408
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005408/suppl/GSM1005408_UB_mouse6_CDX2.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005409 | GPL1261 |
|
Cdx2 induced leukemia_secondary_rep1
|
spleen cells from Cdx2-initiated leukemic animals
|
strain background: C57BL/6
recipient strain: lethally irradiated syngeneic mice
cell source: spleen cells from secondary leukemic animals
injected with: 1x10e6 spleen cells from primary leukemic animal
|
SAMPLE 7
Gene expression data from murine Cdx2-induced myeloid leukemia
|
| Sample_geo_accession | GSM1005409
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005409/suppl/GSM1005409_UB_mouse_11218.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005410 | GPL1261 |
|
Cdx2 induced leukemia_secondary_rep2
|
spleen cells from Cdx2-initiated leukemic animals
|
strain background: C57BL/6
recipient strain: lethally irradiated syngeneic mice
cell source: spleen cells from secondary leukemic animals
injected with: 1x10e6 spleen cells from primary leukemic animal
|
SAMPLE 8
Gene expression data from murine Cdx2-induced myeloid leukemia
|
| Sample_geo_accession | GSM1005410
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005410/suppl/GSM1005410_UB_mouse_11221.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005411 | GPL1261 |
|
Cdx2 induced leukemia_primary rep1
|
spleen cells from Cdx2-initiated leukemic animals
|
strain background: C57BL/6
recipient strain: lethally irradiated syngeneic mice
cell source: spleen cells from primary leukemic animal
injected with: 8x10e5 GFP-positive bone marrow cells (pMSCV-Cdx2-IRES-GFP)
|
SAMPLE 9
Gene expression data from murine Cdx2-induced myeloid leukemia
|
| Sample_geo_accession | GSM1005411
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 |
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005411/suppl/GSM1005411_UB_mouse_CDX2-1.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
|
GSM1005412 | GPL1261 |
|
Cdx2 induced leukemia_primary rep2
|
spleen cells from Cdx2-initiated leukemic animals
|
strain background: C57BL/6
recipient strain: lethally irradiated syngeneic mice
cell source: spleen cells from primary leukemic animal
injected with: 8x10e5 GFP-positive bone marrow cells (pMSCV-Cdx2-IRES-GFP)
|
SAMPLE 10
Gene expression data from murine Cdx2-induced myeloid leukemia
|
| Sample_geo_accession | GSM1005412
| | Sample_status | Public on Dec 21 2012
| | Sample_submission_date | Sep 17 2012
| | Sample_last_update_date | Dec 22 2012
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | Experiment 1 (Samples 1-6): Bone marrow cells were harvested from 3x15 C57BL/6 mice, and differentiated cells were removed by incubation with rat antibodies against lineage antigens (CD3, CD4, CD8, Gr-1, B220, CD19, IL-7R, Ter119) followed by depletion with magnetic beads (Dynabeads, Invitrogen). Lineage-depleted cells were stained with APC-conjugated anti-c-Kit and PE-Cy5-conjugated goat anti-rat antibodies, and c-Kit+ Lin– cells were sorted using a BD FACSAria cell sorter (BD Biosciences). Cells were plated in RetroNectin-coated tissue culture dishes (Takara Bio) and transduced twice with pMSCV-Cdx2-IRES-GFP or pMSCV-IRES-GFP retroviral constructs. After 48 hours, GFP-positive cells were sorted using a BD FACSAria cell sorter.
| | Sample_treatment_protocol_ch1 | Experiment 2 (Samples 7-10): Bone marrow cells isolated from C57BL/6 mice were transduced with pMSCV-Cdx2-IRES-GFP, and 8x10e5 GFP-positive cells were injected into lethally irradiated syngeneic recipient mice after 48 hours, followed by injection of 1x10e6 spleen cells from primary leukemic animals into sublethally irradiated secondary recipients. Spleen cells from secondary leukemic animals were harvested.
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | The total RNA was purified with Qiagen RNeasy Mini kits (Qiagen).
| | Sample_label_ch1 | Biotin
| | Sample_label_protocol_ch1 | For each sample preparation, total RNA was converted into double-stranded cDNA by reverse transcription using the 3' IVT Express Kit from Affymetrix according to the manufacturer's recommendations.
| | Sample_hyb_protocol | Hybridization, washing, and staining protocols, respectively, were performed on Affymetrix GeneChip instruments (Hybridization Oven 640, Fluidics Station FS450) as recommended by the manufacturer.
| | Sample_scan_protocol | Scanning was performed on Affymetrix GeneChip Scanner GCS3000 instruments as recommended by the manufacturer using default settings. The software used was GCOS 1.2 or higher.
| | Sample_data_processing | The data were analyzed with BRB ArrayTools using RMA. Intensity values were log2 transformed
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Lars,,Bullinger
| | Sample_contact_email | lars.bullinger@uniklinik-ulm.de
| | Sample_contact_phone | +49-731-500-45501
| | Sample_contact_fax | +49-731-500-45505
| | Sample_contact_department | Internal Medicine III
| | Sample_contact_institute | University of Ulm
| | Sample_contact_address | Albert-Einstein-Allee 23
| | Sample_contact_city | Ulm
| | Sample_contact_zip/postal_code | 89081
| | Sample_contact_country | Germany
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1005nnn/GSM1005412/suppl/GSM1005412_UB_mouse_CT410.CEL.gz
| | Sample_series_id | GSE40939
| | Sample_data_row_count | 45101
| | |
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