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Sample GSM3735113

Query DataSets for GSM3735113

Status

Public on Sep 20, 2019

Title

07D-0mg_Rep2

Sample type

SRA

Source name

Plantaris tendon

Organism

Rattus norvegicus

Characteristics

strain: Sprague Dawley
surgical repair time: 7 days
gsk2894631a treatment dose: 0mg/kg

Extracted molecule

total RNA

Extraction protocol

Tendons were finely minced, and then placed into 2mL tubes containing 2.3mm steel beads and TRI Reagent (Molecular Research Center, Cincinnati, OH, USA), homogenized for 15 sec, and isolated following product directions. The subsequent RNA pellet was then further cleaned up using miRNeasy kit (Qiagen, Valencia, CA, USA), supplemented with DNase I (Qiagen). RNA concentration was determined using a NanoDrop (ThermoFisher Scientific, Waltham, MA, USA), and quality was assessed using a TapeStation D1000 System (Agilent, Santa Clara, CA, USA). All RNA samples used for sequencing had RIN values > 8.0.
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

Sequencing data was quality checked using FastQC, aligned to the reference genome (Rn6) with the STAR software package
Differential expression based on counts per million mapped reads was performed using edgeR.
Genome_build: Rn6
Supplementary_files_format_and_content: edgeR

Submission date

Apr 24, 2019

Last update date

Sep 20, 2019

Contact name

Christopher L Mendias

Organization name

Hospital for Special Surgery

Street address

535 E 70th St

City

New York