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Status |
Public on May 04, 2021 |
Title |
Y94.617S |
Sample type |
SRA |
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Source name |
skin
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Organism |
Tursiops truncatus |
Characteristics |
Sex: Male location: Barataria Bay, LA sampling date: 2017-06-16 fb field id: Y94
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA was extracted using Qiagen Rneasy Lipid Tissue Mini kits with on-column Dnase digestion. Libraries were constructed using a NEBNext ultra Directional RNA Library Prep kit for Illumina and indexed with the NEBNextMultiplex Oligos for Illumina
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Description |
CARMMHA_skin_GEO_data.xlsx
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Data processing |
The Illumina BCL output files were converted to fastq-sanger file format and sequence quality triming was performed on CyVerse Discovery Environment with the HTProcess-prepare_directories-and-run_fastqc-0.1 and HTProcess_trimmomatic_0.33 apps. The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36. Reads were mapped to the Tursiops truncatus genome, NIST Tru_tru v1 (GCF_001922835.1), on CyVerse Discovery Environment with the HTProcess_Tophat-2.1.1 app using Bowtie as the alignment engine. Read counts as FPKM (fragments per kilobase of trnascript per million mapped reads) were generated on CyVerse Discovery Environment with the HTProcess_Cufflinks-2.2.1 app with the genome as a reference. Genome_build: NIST Tur_tru v1 Supplementary_files_format_and_content: Processed data is supplied in a single file. The first column, "locus", contains the id/location from the NIST Tur_tru v1 genome. The remaining colums contain the FPKM values for each sample as generated by Cufflinks.
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Submission date |
Oct 16, 2019 |
Last update date |
May 04, 2021 |
Contact name |
Jeanine Morey |
Organization name |
National Marine Mammal Foundation
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Department |
Conservation Medicine
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Street address |
3419 Maybank Hwy, Ste B
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City |
Johns Island |
State/province |
SC |
ZIP/Postal code |
29455 |
Country |
USA |
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Platform ID |
GPL27600 |
Series (1) |
GSE138935 |
RNA-seq analysis of archived skin from common bottlenose dolphin health assessments in the northern Gulf of Mexico |
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Relations |
BioSample |
SAMN13039540 |
SRA |
SRX7005007 |
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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