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Sample GSM1976267 Query DataSets for GSM1976267
Status Public on Apr 28, 2016
Title Cho_rep3
Sample type SRA
Source name Primary chondrocyte
Organism Mus musculus
Characteristics cell type: Chondorocytes
isolated from: rib
strain: C57BL/6
age: P1
genotype: WT
Treatment protocol NA
Growth protocol Primary osteoblasts were isolated P1 mouse calvaria and primary chondrocytes were isolated from P1 mouse rib cartilage
Extracted molecule total RNA
Extraction protocol Primary osteoblasts were isolated by 1 unit/ml Liberase TM (05401119001, Roche). Primary chondrocytes were isolated by 2 mg/mL PRONASE Protease (53702, EMD Millipore Corporation) and 0.2% Collagenase D (1088858; Roche Applied Science)
RNA libraries were constructed by Tru-Seq Illumina kit (RS-122-2001, illumina) with some modifications
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
Description Cho_WT3
Data processing The raw reads were first subjected to pre-alignment Quality Assurance and Quality Control (QA/QC).
Any base below a Phred value of 20 was trimmed from either side of the read and reads shorter than 25 nt length were removed.
The processed reads were aligned by Tophat2-2.0.8 (Kim et al., 2013) to mm9 reference genome.
The mapping quality and coverage were checked by post-alignment QA/QC.
Aligned reads were quantified by an expectation maximization algorithm (Xing et al., 2006), followed by a normalization of mapped reads per kilo base length of transcript per million reads (RPKM).
Genome_build: mm9
Supplementary_files_format_and_content: .txt file reports abundance measurements
Submission date Dec 20, 2015
Last update date May 15, 2019
Contact name Hironori Hojo
Phone +81-3-5841-1427
Organization name The University of Tokyo
Department Center for Disease Biology and Integrative Medicine
Lab Clinical Biotechnology
Street address 7-3-1 Hongo
City Bunkyo-ku
State/province Tokyo
ZIP/Postal code 113-8655
Country Japan
Platform ID GPL13112
Series (2)
GSE76186 Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification [RNA-Seq]
GSE76187 Sp7/Osterix is restricted to bone-forming vertebrates where it acts as a Dlx co-factor in osteoblast specification
BioSample SAMN04357105
SRA SRX1492998

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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