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Sample GSM2417039 Query DataSets for GSM2417039
Status Public on Jan 01, 2017
Title Wildtype 2
Sample type SRA
 
Source name Neonatal mouse calavri
Organism Mus musculus
Characteristics strain: C57Bl/6J
cell type: Osteoblast
genotype/variation: Wildtype
Treatment protocol Cells from wildtype and Cdc73/Hrpt2 cKO mice were isolated and sorted uniformily
Growth protocol Calvari were harvested from 5 day-old pups, washed/collagenase digested and strained prior to cell sorting based on transgenic GFP expression controlled by Osteocalcin-Cre. Cells were sorted into Trizol and stored at -80C until RNA isolation
Extracted molecule total RNA
Extraction protocol RNA was isolated using phenol/chloroform and precipitated over night in isopropanol, pelleted, dried and resuspended in water
Library construction was performed by Hudson Alpha
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description wt_2
Data processing Reads were generated on a HiSeq 2500 System and Casava version 1.7 at
Sequenced reads were aligned to the mm10 genome using the subjunc aligner from the Rsubread R package using default parameters
Raw counts for gene-level features were computed using the featureCounts function in the Rsubread package using NCBI RefSeq annotation for mm10 (build 38.1)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file including a matrix of raw counts for each sample
 
Submission date Dec 05, 2016
Last update date May 15, 2019
Contact name Casey James Droscha
Organization name Van Andel Institute
Department Program for Skeletal Disease and Tumor Microenviroment
Lab Cell Signaling & Carcinogenesis
Street address 333 Bostwick Ave.
City Grand Rapids
State/province Michigan
ZIP/Postal code 49503
Country USA
 
Platform ID GPL17021
Series (1)
GSE90890 Osteoblast-specific deletion of Hrpt2/Cdc73 results in high bone mass and increased bone turnover
Relations
BioSample SAMN06111461
SRA SRX2396291

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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