characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2020-03-05T04:05:53Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-02-28T11:48:27Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA101146168
characteristics.characteristic: External Id
characteristics.text: Garvan Institute of Medical Research
characteristics.characteristic: INSDC center name
characteristics.text: 2020-03-05T04:05:53Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-02-28T11:48:27Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1572976
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5533:Clean_1
characteristics.characteristic: Submitter Id
characteristics.text: 10
characteristics.unit: week
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: house mouse
characteristics.characteristic: common name
characteristics.text: Protocols: Mice were sacrificed by CO2 asphyxiation and cervical dislocation. Both humeri were isolated by disarticulation from 5 mice (a total of 10 bone samples). Soft tissue including muscle, ligaments and tendons were removed, before the surface was gently scraped with a scalpel to remove the periosteum. Diaphyseal bone from the humeri was isolated by cutting immediately proximal to the deltoid tuberosity and then 1mm proximal to the epicondyles before completely removing the deltoid tuberosity along the bone shaft. Bone marrow was removed from the left humeri by first flushing with PBS until visibly clean and then centrifuging at 14,000rcf for 15 seconds(\Clean_bone\ samples), whilst the marrow was retained in right humeri (\Bone_and_marrow\ samples). Bones were cut into pieces and snap frozen in liquid N2 prior to homogenisation and RNA extraction. All samples from each mouse were processed and snap frozen in liquid N2 within ~16 minutes of sacrifice. TRIreagent (Sigma T9424) was added directly to the frozen bone samples and homogenised using a Polytron hand held homogeniser (Kinematica PT 1200 E 11010026). RNA was isolated according to the manufacturers protocol and cleaned with an additional ethanol-precipitation step. RNA yield was determined using a Nanodrop (Thermo) and RNA integrity determined using the Bioanalyser RNA 6000 Nano Kit (Agilent Technologies 5067-1511). Total-RNA (250ng) was depleted of ribosomal RNA using RNaseH (Epicentre H39500) and ribosomal RNA targeting oligonucleotides based on a protocol by Adiconis et al., 2013 (Adiconis et al., 2013). Briefly, total RNA, spiked with ERCC internal controls (Life Technologies 4456739), was incubated with ribosomal-RNA targeting oligos and RNaseH to degrade the rRNAs before the oligos were removed with a DNase treatment (Life Technologies AM2238). RNA was repurified using magnetic beads according to the manufacturers protocol (Beckman Coulter Genomics A63987). Total-RNA, 125bp paired-end, stranded transcriptome libraries were prepared using the TruSeq Stranded Total RNA LT Sample Prep Kit starting from the fragmentation step in the manufacturers protocol (Illumina RS-122-2201).
characteristics.characteristic: description
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: 1
characteristics.characteristic: individual
characteristics.text: Mus musculus
characteristics.characteristic: organism
characteristics.text: Mus musculus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_10090
characteristics.characteristic: organism
characteristics.text: humerus
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000976
characteristics.characteristic: organism part
characteristics.text: bone
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0002481
characteristics.characteristic: sampling site
characteristics.text: Mus musculus
characteristics.characteristic: scientific_name
characteristics.text: male
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/PATO_0000384
characteristics.characteristic: sex
characteristics.text: C57BL6/NTac
characteristics.characteristic: strain
characteristics.text: Clean_1
characteristics.characteristic: title