|
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
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|
|
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
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|
|
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 |