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Sample GSM3591839 Query DataSets for GSM3591839
Status Public on Jun 10, 2019
Title Sample_45866
Sample type SRA
 
Source name hindlimb tendon
Organism Mus musculus
Characteristics condition: 2 - Tenotomy site of a burn/tenotomy mouse (3 weeks after injury)
strain: C57BL/6 background
timepoint: three week tenotomy sites after burn tenotomy
Treatment protocol A partial-thickness scald burn injury was administered to animals according to a previously described protocol by a single surgeon.3,57 Briefly, mice were anesthetized with inhaled isoflurane. Dorsal hair was closely clipped, and an aluminum block heated to 60°C was exposed to the dorsal region over 30% of the total body surface area for 18 s to achieve a partial-thickness burn injury. Each mouse then received a concurrent sterile dorsal hind limb tendon transection at the midpoint of the Achilles tendon (Achilles tenotomy) with placement of a single 5-0 vicryl suture to close the skin. Pain management was achieved with subcutaneous injections of buprenorphine (Buprenex, Reckitt Benckiser Pharmaceuticals) every 12 hr for 2 days.
Extracted molecule total RNA
Extraction protocol Tissue was harvested from the Tenotomy site: between the insertion point in the gastrocnemius muscle and the attachment of the tendon at the calcaneous. Total RNA was extracted using Trizol™ reagent, and subsequently purified using a RNAeasy kit from Qiagen. RNA purity was confirmed before sequencing. Condition 1 is the uninjured right leg from the B/T, condition 2 is the injured left leg of B/T, and condition 3 is from uninjured WT non-B/T mouse.
TruSeq RNA-prep kit, according to manufacturer's protocol
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Condition 2: Tenotomy site of a burn/tenotomy mouse (3 weeks after injury)
Data processing The quality of the fastq files from the sequencer were first checked using FastQC (v0.11.4).
used Kallisto to extract expression matrix
Genome_build: GRCh38
Supplementary_files_format_and_content: Data matrix table is in text format
 
Submission date Feb 05, 2019
Last update date Jun 10, 2019
Contact name Rajasree Menon
E-mail(s) rajmenon@umich.edu
Phone 7346159720
Organization name University of Michigan
Department Department of Computational Medicine and Bioinformatics
Street address 4544E, MSRB2, Catherine Street, University of Michigan
City Ann Arbor
State/province Michigan
ZIP/Postal code 48109
Country USA
 
Platform ID GPL13112
Series (1)
GSE126118 Coordinating Tissue Regeneration through TGF-β Activated Kinase 1 (TAK1) In-activation and Re-activation
Relations
BioSample SAMN10877785
SRA SRX5336836

Supplementary file Size Download File type/resource
GSM3591839_Sample_45866.tsv.gz 1.4 Mb (ftp)(http) TSV
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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