Comment[GEAAccession]	E-GEAD-293
MAGE-TAB Version	1.1
Investigation Title	Search for protease capable of degrading osteoprotegerin in the bone microenvironment.
Experiment Description	To search genes up-regulated during differentiation from BMM into osteoclasts were selected as candidates for osteoprotegerin (OPG) -degrading enzymes, we performed the RNA-sequencing analysis.
Experimental Design	cell type comparison design	replicate design
Experimental Factor Name	cell type
Experimental Factor Type	cell type
Person Last Name	Nakachi	Ochiai	Suda
Person First Name	Yutaka	Nagahiro	Tatsuo
Person Affiliation	Research Center for Genomic Medicine, Saitama Medical University		
Person Roles	submitter	submitter	submitter
Public Release Date	2019-03-19
Protocol Name	P-GEAD-77	P-GEAD-78	P-GEAD-79	P-GEAD-80	P-GEAD-81
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Bone marrow-derived macrophages were obtaioned from 10-week-old male and newborn ICR mice. Osteoclasts were derived from those BMM-macrophages by cultured for 3 days in osteoblast-condition medium in the presence of M-CSF together with RANKL.	Total RNA was extracted from BMM and OC using TRIzol reagents (Thermo Fisher Scientific) according to the manufacturer's instructions.	Sequencing libraries of BMM and OC (total of 4 libraries) were constructed using TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego, CA).	The RNA sequencing data were obtained using Illumina HiSeq 2500 sequencer with 100 bp paired-end reads, according to the manufacturer's instructions.	All the sequence data were mapped to Mus musculus reference sequence (GRCm38, Genome Reference Consortium) with Tophat2/Bowtie2 (v2.1.0/2.2.8, respectively). The number of sequence reads corresponding to each gene model (Ensembl release 80) was counted by cufflinks v2.2.1.  Detection of differentially expressed genes was performed by HTSeq (0.6.1) and edgeR (3.8.6).
SDRF File	E-GEAD-293.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB7826
Comment[Last Update Date]	2019-08-14