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| Status |
Public on Nov 18, 2020 |
| Title |
M_tick3 |
| Sample type |
SRA |
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| Source name |
Whole body of the tick
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| Organism |
Dermacentor marginatus |
| Characteristics |
state: newly molted for 5 days
tick strain: laboratory reared F2 generation
Sex: female
age: adult
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Ticks were pulverized in liquid nitogen, then total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA(5ug) using poly-T oligo-attached magnetic beads by two rounds of purification. Then the left RNA was fragmented into small pieces using divalent cations under elevated temperature.The cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the TruSeq Stranded Total RNA HT Sample Prep Kit (Illumina, San Diego, USA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Description |
pooled sample of 5 ticks
gene_expression.txt
Trinity.gene.fasta
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| Data processing |
Illumina Casava1.8 software used for basecalling.
Firstly, Cutadapt 2.6 was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases;
Then denovo assembly of the transcriptome was performed with Trinity , and salmon was used to perform expression level for unigenes by calculating TPM;
All assembled unigenes were aligned against the non-redundant (Nr) protein database (http://www.ncbi.nlm.nih.gov/),Gene ontology (GO) (http://www.geneontology.org), SwissProt (http://www.expasy.ch/sprot/), Kyoto Encyclopedia of Genes and Genomes (KEGG) (http://www.genome.jp/kegg/), Protein family (Pfam) (http://pfam.xfam.org/) and eggnog (http://eggnogdb.embl.de/) databases using DIAMOND with a threshold of E value < 0.00001.
Supplementary_files_format_and_content: tab-delimited text file include TPM values and fasta file including all trinity gene sequences
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| Submission date |
Jun 02, 2020 |
| Last update date |
Nov 19, 2020 |
| Contact name |
Ercha Hu |
| E-mail(s) |
[email protected]
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| Phone |
+8615099493210
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| Organization name |
Xinjiang Agricultural University
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| Department |
College of Veterinary
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| Street address |
Nongda east Rd311
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| City |
Urumqi |
| State/province |
Xinjiang |
| ZIP/Postal code |
830052 |
| Country |
China |
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| Platform ID |
GPL28620 |
| Series (1) |
| GSE151667 |
Dermacentor marginatus female adults transcriptome |
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| Relations |
| BioSample |
SAMN15086211 |
| SRA |
SRX8455371 |
| 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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