Search results for the GEO ID: GSE12538  |
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|
GSM ID | GPL ID |
Select for analysis |
Title |
Source name |
Description |
Characteristics |
GSM313206 | GPL1261 |
|
HSC_Control_1
|
Lin-Sca1+CD150+CD48-HSCs_Control
|
Mouse model: c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48-)
|
HSC_Control_1
|
| Sample_geo_accession | GSM313206
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 16 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM313nnn/GSM313206/suppl/GSM313206.CEL.gz
| | Sample_series_id | GSE12467
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM313207 | GPL1261 |
|
HSC_Control_2
|
Lin-Sca1+CD150+CD48-HSCs_Control2
|
Mouse model: c-myc f2 M-Myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48-)
|
HSC_Control_2
|
| Sample_geo_accession | GSM313207
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 16 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM313nnn/GSM313207/suppl/GSM313207.CEL.gz
| | Sample_series_id | GSE12467
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM313208 | GPL1261 |
|
HSC_Control_3
|
Lin-Sca1+CD150+CD48-HSCs_Control3
|
Mouse model: c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48-)
|
HSC_Control_3
|
| Sample_geo_accession | GSM313208
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 16 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM313nnn/GSM313208/suppl/GSM313208.CEL.gz
| | Sample_series_id | GSE12467
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM313209 | GPL1261 |
|
HSC_dKO_1
|
Lin-Sca1+CD150+CD48-HSCs_dKO1
|
Mouse model: MxCre c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48-)
|
HSC_dKO_1
|
| Sample_geo_accession | GSM313209
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 16 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM313nnn/GSM313209/suppl/GSM313209.CEL.gz
| | Sample_series_id | GSE12467
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM313210 | GPL1261 |
|
HSC_dKO_2
|
Lin-Sca1+CD150+CD48-HSCs_dKO2
|
Mouse model: MxCre c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48-)
|
HSC_dKO_2
|
| Sample_geo_accession | GSM313210
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 16 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM313nnn/GSM313210/suppl/GSM313210.CEL.gz
| | Sample_series_id | GSE12467
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM313211 | GPL1261 |
|
HSC_dKO_3
|
Lin-Sca1+CD150+CD48-HSCs_dKO3
|
Mouse model: MxCre c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48-)
|
HSC_dKO_3
|
| Sample_geo_accession | GSM313211
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 16 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM313nnn/GSM313211/suppl/GSM313211.CEL.gz
| | Sample_series_id | GSE12467
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM315272 | GPL1261 |
|
Progen_Control_1
|
Lin-Sca1+CD150+CD48+Progen_Control1
|
Mouse model: c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow LT-HSCs (Lin- Sca1+ CD150+ CD48+)
|
Progen_Control_1
|
| Sample_geo_accession | GSM315272
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 24 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_data_processing |
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315272/suppl/GSM315272.CEL.gz
| | Sample_series_id | GSE12536
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM315273 | GPL1261 |
|
Progen_Control_2
|
Lin-Sca1+CD150+CD48+Progen_Control2
|
Mouse model: c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow progenitor cells (Lin- Sca1+ CD150+ CD48+)
|
Progen_Control_2
|
| Sample_geo_accession | GSM315273
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 24 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_data_processing |
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315273/suppl/GSM315273.CEL.gz
| | Sample_series_id | GSE12536
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM315274 | GPL1261 |
|
Progen_Control_3
|
Lin-Sca1+CD150+CD48+Progen_Control3
|
Mouse model: c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow progenitor cells (Lin- Sca1+ CD150+ CD48+)
|
Progen_Control_3
|
| Sample_geo_accession | GSM315274
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 24 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_data_processing |
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315274/suppl/GSM315274.CEL.gz
| | Sample_series_id | GSE12536
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM315275 | GPL1261 |
|
Progen_dKO_1
|
Lin-Sca1+CD150+CD48+Progen_dKO1
|
Mouse model: MxCre c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow progenitor cells (Lin- Sca1+ CD150+ CD48+)
|
Progen_dKO_1
|
| Sample_geo_accession | GSM315275
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 24 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_data_processing |
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315275/suppl/GSM315275.CEL.gz
| | Sample_series_id | GSE12536
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM315276 | GPL1261 |
|
Progen_dKO_2
|
Lin-Sca1+CD150+CD48+Progen_dKO2
|
Mouse model: MxCre c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow progenitor cells (Lin- Sca1+ CD150+ CD48+)
|
Progen_dKO_2
|
| Sample_geo_accession | GSM315276
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 24 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_data_processing |
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315276/suppl/GSM315276.CEL.gz
| | Sample_series_id | GSE12536
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
|
GSM315277 | GPL1261 |
|
Progen_dKO_3
|
Lin-Sca1+CD150+CD48+Progen_dKO3
|
Mouse model: MxCre c-myc f2 N-myc f2 on a mixed background
Age: 8 weeks old
Tissue: Bone marrow progenitor cells (Lin- Sca1+ CD150+ CD48+)
|
Progen_dKO_3
|
| Sample_geo_accession | GSM315277
| | Sample_status | Public on Feb 20 2009
| | Sample_submission_date | Aug 24 2008
| | Sample_last_update_date | Feb 20 2009
| | Sample_type | RNA
| | Sample_channel_count | 1
| | Sample_organism_ch1 | Mus musculus
| | Sample_taxid_ch1 | 10090
| | Sample_treatment_protocol_ch1 | 2 daily pI-pC treatment, last treatment 3 days prior to sacrifice
| | Sample_molecule_ch1 | total RNA
| | Sample_extract_protocol_ch1 | RNA from sorted cells was purified using Trizol extraction followed by ethanol precipitation and 2 rounds of amplification with the Nugen WT-Ovation Pico RNA Amplification System.
| | Sample_label_ch1 | biotin
| | Sample_label_protocol_ch1 | See Affymetrix GeneChip® Two-Cycle Target Labeling Assay protocol, Affymetrix GeneChip ® IVT labeling kit
| | Sample_hyb_protocol | Affymetrix GeneChip® Hybridization Control Kit
| | Sample_scan_protocol | Gene Chip Scanner 3000 (Affymetrix) running GCOS 1.1.1 software.
| | Sample_data_processing = Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE | GSM315273
| | Sample_data_processing = Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE | GSM315274
| | Sample_data_processing = Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE | GSM315275
| | Sample_data_processing = Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE | GSM315276
| | Sample_data_processing = Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.^SAMPLE | GSM315277
| | Sample_data_processing | Quality control tests were performed utilizing the DNA Array Facility of Lausanne’s Remote Analysis System (http://race.unil.ch), a web-based interface for various statistical analysis routines performed utilizing the R language (http://www.r-project.org). Various quality tests were performed: comparison of RNA 5’ end to 3’end bias utilizing RNA degradation plots to determine the quality of amplification; density of PM intensities; RMA normalization of the chips; sample clustering to control replicates; correlation matrix to observe correlation between samples and replicates; surface intensity in log scale to examine for chip and hybridization defects; scatter plots to compare samples and replicates. RMA normalized data was entered into the Genespring program (Silicon Genetics) for data visualization as well as further filtering and examination of overlaps of various gene lists.
| | Sample_platform_id | GPL1261
| | Sample_contact_name | Elisa,,Laurenti
| | Sample_contact_email | elisa.laurenti@epfl.ch
| | Sample_contact_phone | 0041216925816
| | Sample_contact_laboratory | Trumpp
| | Sample_contact_department | ISREC
| | Sample_contact_institute | EPFL
| | Sample_contact_address | Chemin Des Boveresses 155
| | Sample_contact_city | Epalinges
| | Sample_contact_zip/postal_code | 1066
| | Sample_contact_country | Switzerland
| | Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM315nnn/GSM315277/suppl/GSM315277.CEL.gz
| | Sample_series_id | GSE12536
| | Sample_series_id | GSE12538
| | Sample_data_row_count | 45101
| | |
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