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| Status |
Public on Dec 06, 2016 |
| Title |
TYP140227-04 |
| Sample type |
SRA |
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| Source name |
skin
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| Organism |
Tursiops truncatus |
| Characteristics |
tissue: skin
Sex: male
collection_date: 2014-02-27
geo_loc_name: USA:Cooper, Ashley, Wando, and Stono River Basin (CAWS), South Carolina
lat_lon: 32.72742_-79.80157
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| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen RNeasy Lipid Tissue Mini Kit with on-column DNase digestion.
NEBNext Ultra Directional RNA Library Prep Kit for Illumina, indexed with the NEBNextMulitplex Oligos for Illumina.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Illumina BCL output files were converted to FASTQ-sanger file format in Galaxy with FASTQ Groomer. Sequence quality trimming was performed using Trimmomatic with a minimum quality score of phred >20 over the length of the reads. The trimmed reads were then quality checked using the FASTQC tool.
Reads were mapped to the Ensembl T. truncatus genome, version turTru1 v76.1, with Bowtie2 v 2.2.4 as the alignment engine within the package RNA-Seq by Expectation Maximization (RSEM), generating mapped read counts as FPKM (fragments per kilobase of transcript per million mapped reads).
A table of summarized FPKMs for all samples was created.
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| Submission date |
Dec 06, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Marion Neely |
| E-mail(s) |
marion.neely@gmail.com
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| Organization name |
National Ocean Services
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| Department |
NCCOS
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| Lab |
Marine Genomics Core Facility
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| Street address |
331 Ft. Johnson Rd
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| City |
Charleston |
| State/province |
SC |
| ZIP/Postal code |
29412 |
| Country |
USA |
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| Platform ID |
GPL21538 |
| Series (1) |
| GSE90941 |
Skin Transcriptomics of Common Bottlenose Dolphins (Tursiops truncatus) from the Northern Gulf of Mexico and Southeastern U.S. Atlantic Coasts |
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| Relations |
| BioSample |
SAMN06113358 |
| SRA |
SRX2398822 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2417904_TYP140227-04_CHS_FP0RSEM_genome.genes.results.txt.gz |
293.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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