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Sample GSM4118918 Query DataSets for GSM4118918
Status Public on May 04, 2021
Title 223.16B
Sample type SRA
 
Source name blood
Organism Tursiops truncatus
Characteristics tissue: blood
Sex: Female
location: Sarasota Bay, FL
sampling date: 2016-05-11
fb field id: 223
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
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description CARMMHA_blood_GEO_data.xlsx
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.
 
Submission date Oct 11, 2019
Last update date May 05, 2021
Contact name Jeanine Morey
Organization name National Marine Mammal Foundation
Department Conservation Medicine
Street address 3419 Maybank Hwy, Ste B
City Johns Island
State/province SC
ZIP/Postal code 29455
Country USA
 
Platform ID GPL27600
Series (1)
GSE138765 RNA-seq analysis of archived blood from common bottlenose dolphin health assessments in the northern Gulf of Mexico
Relations
BioSample SAMN13019175
SRA SRX6980671

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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