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| Status |
Public on Apr 25, 2019 |
| Title |
Mus_Day-7_rep2 |
| 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_4
mus7.4
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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 |
SAMN08922535 |
| SRA |
SRX3929675 |
| 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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