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| Status |
Public on Jul 11, 2016 |
| Title |
MSCB7_Veh_rep1 |
| Sample type |
SRA |
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| Source name |
marrow derived MSC
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| Organism |
Mus musculus |
| Characteristics |
cell type: marrow-derived mesenchymal stem cells
differentiation time point (day): 7
differentiation media: osteogenic
treatment: vehicle
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| 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.
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| 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.
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Apr 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Mark B Meyer |
| E-mail(s) |
markmeyer@wisc.edu
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| Phone |
608-890-0857
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| Organization name |
University of Wisconsin-Madison
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| Department |
Nutritional Sciences
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| Lab |
Meyer Lab
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| Street address |
1415 Linden Dr.
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| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53706 |
| Country |
USA |
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| 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 |
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| Relations |
| BioSample |
SAMN04599677 |
| SRA |
SRX1672939 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2104264_MSCB7_Veh_rep1_RPKM.txt.gz |
150.7 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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