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Status |
Public on May 04, 2021 |
Title |
294.16B |
Sample type |
SRA |
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Source name |
blood
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Organism |
Tursiops truncatus |
Characteristics |
tissue: blood Sex: Male location: Sarasota Bay, FL sampling date: 2016-05-11 fb field id: 294
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Extracted molecule |
total RNA |
Extraction protocol |
Whole blood RNA was extracted using a PAXgene Blood RNA Kit (Qiagen). 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_blood_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. Sequences annotated as hemoglobin were masked from alignment. 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. Sequences annotated as hemoglobin were masked from analysis. 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 11, 2019 |
Last update date |
May 05, 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) |
GSE138765 |
RNA-seq analysis of archived blood from common bottlenose dolphin health assessments in the northern Gulf of Mexico |
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Relations |
BioSample |
SAMN13019193 |
SRA |
SRX6980678 |
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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