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| Status |
Public on Dec 02, 2015 |
| Title |
Tc-CKrep3 |
| Sample type |
SRA |
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| Source name |
T. cinnabarinus_control_2d-old adult mite tissue
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| Organism |
Tetranychus cinnabarinus |
| Characteristics |
treated with: none (field population control)
strain phenotype: susceptible strain
developemental stage: 2-day old adult mite
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 2 day-old adult mites using the RNeasy plus Micro Kit (Qiagen, Hilden, Germany). Genomic DNA was removed using a genomic DNA elimination column supplied with the kit.
The Ribosomal RNA depletion was carried out using RiboMinus RNA plant kit for RNA-Seq (Life Technologies, CA). The whole transcriptome cDNA library was prepared using Ion Total RNA-Seq kit V2 (Life Technologies Corporation, CA).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
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| Data processing |
Processing of raw data, removal of the adapter sequences, base-calling and quality value calculations were performed using Torrent Suite™ Software 4.0 (Ion torrent, Life technologies, CA).
The whole transcriptome cDNA library was prepared using Ion Total RNA-Seq kit V2 (Life Technologies Corporation, CA).
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to the T. urticae genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Clean reads are the high quality sequences after data cleaning, on which all following analyses are based.
The entire assembled genes were used to search for the best-hit homologous proteins (BLASTX cut-off e-value 1.0E-5) in the T. urticae genome
For interlibrary comparison, read numbers were normalized to relative abundance as reads per kilobase transcriptome per million mapped reads (RPKM).
Genome_build: Tetranychus urticae genome (database web link: http://bioinformatics.psb.ugent.be/orcae/overview/Tetur)
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
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| Submission date |
Nov 30, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Lu Wencai |
| E-mail(s) |
253953014@qq.com
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| Organization name |
Southwest University
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| Street address |
216 Tiansheng Road
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| City |
Chongqing |
| ZIP/Postal code |
400716 |
| Country |
China |
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| Platform ID |
GPL21192 |
| Series (1) |
| GSE75529 |
Next Generation Sequencing Facilitates Quantitative Analysis of Tetranychus urticae and Its Sibling Species Tetranychus cinnabarinus Transcriptomes |
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| Relations |
| BioSample |
SAMN04302857 |
| SRA |
SRX1456447 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1958577_Tc-CK3.Gene.rpkm.txt.gz |
205.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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