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| Status |
Public on May 11, 2017 |
| Title |
DLBB12-06 |
| Sample type |
SRA |
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| Source name |
blood
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| Organism |
Delphinapterus leucas |
| Characteristics |
date: 2012-09-10
Sex: Male
latitude: 58.950467
longitude: -158.501517
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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 HiSeq 2500 |
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| Description |
DLBB_blood_GEO_data.xls
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| Data processing |
The Illumina BCL output files were converted to fastq-sanger file format and sequence quality triming was performed using Trimmomatic on iPlant Collaborative's Discovery Environment using the High-Performance Computing applications. The following Trimmomatic parameters were used: ILLUMINACLIP:TruSeq3-SE.fa 2:30:10; LEADING:10; TRAILING:10; SLIDINGWINDOW:4:20; HEADCROP:6; MINLEN:36.
The read files from one male (DLBB13-02) and one female (DLBB13-07) animal were concatenated into a single fastq file for assembly in Trinity v2.0.4 using a minimum K-mer coverage of 3, a minimum overlap value of 25 and a minimum contig length of 400 nucleotides on the CyVerse Atmosphere cloud computing platform.
Annotation of the de novo assembly was obtained by BLASTx searches of the human subset of the uniprot_swissprot database augmented with conserved domian mapping and gene ontology assignment using Blast2GO.
Reads were mapped to the de novo Trinity assembly, using RSEM v 1.2.21 with bowtie2 as the alignment engine and read counts were generated as TPM (transcripts per million) at the gene level on the CyVerse Atmosphere cloud computing platform.
Supplementary_files_format_and_content: Processed data is supplied in a single file. The first column "Gene ID" contains the gene ID from the de novo Trinity assembly. The second column "Accession Number" contains the accession number of the top hit from BLASTx searches of the human subset of the UniProt-SwissProt database. The third column "Entrez Gene ID" contains the Entrez Gene ID, if assigned, following BLASTx searches and Blast2GO annotation. The remaining columns contain the TPM values for each sample as generated by RSEM. A TPM > 0 in at least half the samples and an average TPM ≥ 1 across all samples was required for all further data analysis. Only genes meeting these requirements are included in the processed data table.
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| Submission date |
May 09, 2017 |
| Last update date |
May 15, 2019 |
| 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 |
GPL23455 |
| Series (1) |
| GSE98735 |
RNA-seq analysis of blood transcriptomes from beluga whales in Bristol Bay, Alaska, USA |
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| Relations |
| BioSample |
SAMN06925952 |
| SRA |
SRX2794555 |
| 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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