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Sample GSM3096108 Query DataSets for GSM3096108
Status Public on Apr 25, 2019
Title Mus_Day-7_rep1
Sample type SRA
 
Source name Dermal skin (dorsal) - Wound
Organism Mus musculus
Characteristics strain/background: CD-1
age: Adult
tissue: Dermal skin (dorsal)
treatment: Wounded
time point: Day 7
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.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NextSeq 500
 
Description Day 7 wound.
musDay7_1
mus7.1
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.
 
Submission date Apr 12, 2018
Last update date Apr 25, 2019
Contact name Jason Orr Brant
E-mail(s) jobrant@ufl.edu
Organization name University of Florida
Department Biology
Lab Maden
Street address 2033 Mowry Rd
City Gainesville
State/province FL
ZIP/Postal code 32610
Country USA
 
Platform ID GPL19057
Series (1)
GSE113081 Comparative Transcriptomic Analysis of Dermal Wound Healing Reveals De Novo Skeletal Muscle Regeneration in Acomys cahirinus
Relations
BioSample SAMN08922536
SRA SRX3929674

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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