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Sample GSM2104279 Query DataSets for GSM2104279
Status Public on Jul 11, 2016
Title MSCF7_125_rep1
Sample type SRA
 
Source name marrow derived MSC
Organism Mus musculus
Characteristics cell type: marrow-derived mesenchymal stem cells
differentiation time point (day): 7
differentiation media: adipogenic
treatment: 1,25(OH)2D3
Treatment protocol MSC cells were differentiated to days 0, 7, and 15 were treated with 100nM of 1,25(OH)2D3 (or ethanol vehicle) for 24 hours prior to RNA harvesting.
Growth protocol Marrow derived MSC (mdMSC) were obtained from Dr. Janet Rubin, cryopreserved and expanded no more than 10 passages. The MSCs were cultured in minimum Eagle’s medium alpha (MEMα) modification supplemented with 10% fetal bovine serum from Hyclone (Logan, UT), and 1% penicillin-streptomycin from Invitrogen.  For differentiation, cells were grown to confluency and then transferred to either osteogenic differentiation media (10 mM β–glycerophosphate and 50 µg/mL ascorbic acid) or adipogenic differentiation media (5 µg/mL insulin, 50 µM indomethacin, 0.1 µM dexamethasone) for the indicated lengths, replenishing the media every 2-3 days until assay. 
Extracted molecule total RNA
Extraction protocol RNA was isolated using the TRI-Regent protocol (MRC, Cincinnati, OH) with an additional LiCl extraction. Eight μg of total RNA was DNase1 treated (Invitrogen) then ribosomal RNA was depleted using the RiboMinus Eukaryote Kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions
Directional RNA-seq libraries were prepared with the Epicentre (Madison, WI) ScriptSeq v2 RNA-seq Library Preparation Kit per manufacturer’s instructions. Ribosomal RNA depletion (RNA 6000 Nano Kit) and final library quality (High Sensitivity DNA kit) was analyzed with the Agilent Bioanalyzer (Agilent, Santa Clara, CA).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Data processing TopHat with default settings and sample type "fr-secondstrand" for directional libraries
ArrayStar (DNASTAR) with default RNA sequencing settings. Imported BAM files from TopHat output.
Genome_build: mm9
Supplementary_files_format_and_content: tab deliminated text files include RPKM values for each sample
 
Submission date Apr 01, 2016
Last update date May 15, 2019
Contact name Mark B Meyer
E-mail(s) markmeyer@wisc.edu
Phone 608-890-0857
Organization name University of Wisconsin-Madison
Department Nutritional Sciences
Lab Meyer Lab
Street address 1415 Linden Dr.
City Madison
State/province WI
ZIP/Postal code 53706
Country USA
 
Platform ID GPL13112
Series (2)
GSE79814 Epigenetic Plasticity Drives Adipogenic and Osteogenic Differentiation of Marrow-Derived Mesenchymal Stem Cells (RNA-seq)
GSE79815 Epigenetic Plasticity Drives Adipogenic and Osteogenic Differentiation of Marrow-Derived Mesenchymal Stem Cells
Relations
BioSample SAMN04599692
SRA SRX1672954

Supplementary file Size Download File type/resource
GSM2104279_MSCF7_125_rep1_RPKM.txt.gz 151.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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