| Sample_geo_accession | GSM1056849
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| Sample_status | Public on Dec 22 2012
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| Sample_submission_date | Dec 21 2012
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| Sample_last_update_date | Dec 22 2012
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| Sample_type | RNA
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| Sample_channel_count | 1
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| Sample_organism_ch1 | Mus musculus
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| Sample_taxid_ch1 | 10090
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| Sample_treatment_protocol_ch1 | In order to deliver the human Dkk1 gene into MOS-J cells, lentiviral particles were produced using the pLenti6/V5 Directional TOPO Cloning Kit and ViraPower Lentiviral Expression System (Invitrogen). Clones were selected for G418 resistance. For non-viral transfection, human Dkk1 cDNA was cloned into the pLenti6.1 plasmid (Invitrogen) by standard methods. One million MOS-J cells were transfected with a NucleofectorII (Amaxa) using the manufacturer’s settings for Ewing sarcoma cells. Stable lines were generated by Blasticidin S selection. To follow tumor development in vivo, the transfected MOS-J cells were subsequently transduced with a lentiviral construct encoding dsRed-mito driven by the cytomegalovirus promoter (pDsRed2-Mito, BD Biosciences) to fluorescently label mitochondria. To achieve >99% purity, cells were enriched using a MoFlo XDP cell sorter (Beckman Coulter).
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| Sample_growth_protocol_ch1 | murine osteosarcoma cell line MOS-J (Joliat et al. 2002); The Jackson Laboratory at Bar Harbor) were expanded in medium consisting of αMEM, 10% FBS, 100 units ⋅ mL-1 penicillin G, and 100 µg ⋅ mL-1 streptomycin (Invitrogen).
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| Sample_molecule_ch1 | total RNA
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| Sample_extract_protocol_ch1 | Total RNA was extracted from cell pellets using the HighPure RNA Isolation kit (Roche) following the manufacturer’s protocol. RNA quality was assessed by spectrophotometry and PCR for murine GAPDH after reverse transcription using the SuperScript III kit (Invitrogen).
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| Sample_label_ch1 | Biotin
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| Sample_label_protocol_ch1 | Biotinylated cRNA were prepared according to the 3' Express IVT protocol (Affymetrix) from 500 ng of total RNA.
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| Sample_hyb_protocol | Following fragmentation, 15 ug of cRNA were hybridized for 16 hr at 45C onMouse Genome 430 2.0 Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450 using the Affymetrix Hybridization, Wash and Stain Kit.
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| Sample_scan_protocol | GeneChips were scanned using the GeneChip Scanner (Affymetrix)
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| Sample_data_processing | The data were analyzed with MAS5.0 algorithm
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| Sample_platform_id | GPL1261
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| Sample_contact_name | Joni,,Ylostalo
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| Sample_contact_email | ylostalo@medicine.tamhsc.edu
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| Sample_contact_department | Institute for Regenerative Medicine
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| Sample_contact_institute | Texas A&M
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| Sample_contact_address | 5701 Airport Rd., Module C
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| Sample_contact_city | Temple
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| Sample_contact_state | TX
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| Sample_contact_zip/postal_code | 76502
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| Sample_contact_country | USA
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| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1056nnn/GSM1056849/suppl/GSM1056849_ulf-control_Mouse430_2_.020711.mas5.CHP.gz
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| Sample_supplementary_file | ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM1056nnn/GSM1056849/suppl/GSM1056849_ulf-control_Mouse430_2_.CEL.gz
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| Sample_series_id | GSE43112
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| Sample_data_row_count | 45101
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