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Status |
Public on Apr 25, 2019 |
Title |
Mus_Day-7_rep1 |
Sample type |
SRA |
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Source name |
Dermal skin (dorsal) - Wound
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Organism |
Mus musculus |
Characteristics |
strain/background: CD-1 age: Adult tissue: Dermal skin (dorsal) treatment: Wounded time point: Day 7
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Treatment protocol |
8mm full-thickness excisional dorsal dermal wounds. Wounds collected days 7 and 14 after wounding. Wounds compared to day 0, unwounded, normal skin samples for each species.
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was extracted following Trizol protocol and cleaned using Qiagen's RNeasy mini kit. Libraries were prepared using Illumina's TruSeq RNA Sample Preparation kits. 2x150bp paired-end.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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Description |
Day 7 wound. musDay7_1 mus7.1
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Data processing |
Raw reads were quality assessed pre- and post-filtering using FastQC [fastqc/0.11.4] and trimmed using Trimmomatic [trimmomatic/0.32, ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10 HEADCROP:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:40]. Trimmed reads were merged using SeqPrep [seqprep/1.1, -L 40 -n 0.95 -o 25] resulting in both unmerged paired-end reads and merged reads. Acomys merged and paired-end RNA-Seq reads from all three time-points, plus the DSN library, were assembled using Trinity [trinity/2.0.4, --SS_lib_type FR --min_contig_length 500], with in silico normalization at 50X coverage to remove systemic variation. Trinotate [trinotate/2.0.1], which utilizes a variety of homology searches to publicly available data to identify homologous sequences (SwissProt/UniRef90), protein domains (HMMER/PFAM), rRNA (RNAMMER), protein signal peptides and transmembrane domains (signalp/tmHMM). The annotation report only includes hits meeting a minimum E-value cutoff of 1E-5. Transcript abundance estimates were obtained using RSEM [rsem/1.2.28, --paired-end --bowtie2 --estimate-rspd --append-names]. Genome_build: mm9 (MGSCv37) Supplementary_files_format_and_content: aco_vs_mus_genes_counts_matrix.txt: Tab-delimited text file; Count matrix for the COREs between Mus and Acomys for each time-point. Supplementary_files_format_and_content: aco_per_se_genes_counts_matrix.txt: Tab-delimited text file; Count matrix for Acomys for days 0, 7 and 14. Supplementary_files_format_and_content: mus_per_se_genes_counts_matrix.txt: Tab-delimited text file; Count matrix for Mus for days 0, 7 and 14. Supplementary_files_format_and_content: Trinity.fasta: FASTA file includes the Acomys cahirinus transcriptome assembly with Trinity IDs. Supplementary_files_format_and_content: acomys_annotation.txt: Tab-delimited text file lists the Trinity IDs and annotations.
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Submission date |
Apr 12, 2018 |
Last update date |
Apr 25, 2019 |
Contact name |
Jason Orr Brant |
E-mail(s) |
jobrant@ufl.edu
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Organization name |
University of Florida
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Department |
Biology
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Lab |
Maden
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Street address |
2033 Mowry Rd
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City |
Gainesville |
State/province |
FL |
ZIP/Postal code |
32610 |
Country |
USA |
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Platform ID |
GPL19057 |
Series (1) |
GSE113081 |
Comparative Transcriptomic Analysis of Dermal Wound Healing Reveals De Novo Skeletal Muscle Regeneration in Acomys cahirinus |
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Relations |
BioSample |
SAMN08922536 |
SRA |
SRX3929674 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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