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SRX10505517: RNA-Seq of Parakanthophoreus sp.
1 ILLUMINA (NextSeq 500) run: 19.4M spots, 5.8G bases, 2.6Gb downloads

Design: Sample preservation, RNA extraction, sequencing and assembly were conducted based on methods previously described for spiders (Kono, et al. 2016), with some modifications. Briefly, a single specimen of each tanaidacean was preserved in RNAlater Stabilization Solution, then stored at -80 C. RNA was extracted using a Direct-zol RNA Microprep Kit (Zymo Research). The Illumina library was prepared using the KAPA RNA HyperPrep Kit (KAPA Biosystems) targeting 300 bp fragments, but in order to amplify larger silk-related transcripts, PCR extension time was increased to 3 min per cycle. Extracted RNA was below minimum requirement for KAPA RNA HyperPrep Kit for samples R05 Apseudomorpha sp., R06 Paradoxapseudes littoralis, and R24 Heterotanoides sp., and therefore these samples were prepared using SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Clonetech) also with increased PCR extension time, followed by KAPA HyperPlus Kit (KAPA Biosystems) fragmentation and cDNA library preparation. The sequence library was then sequenced on a NextSeq 500 (Illumina) with 300 cycles of high-output mode as paired-end reads. Sequences were base called and demultiplexed, and adaptor sequences were removed with bcls2fastq v.2 software (Illumina).
Submitted by: Keio University
Study: Comprehensive transcriptome sequencing of Tanaidacea with proteomic evidences for their silk
show Abstracthide Abstract
Tanaidaceans are small benthic crustaceans that mainly inhabit diverse marine environments, and they comprise one of the most diverse and abundant macrofaunal groups in the deep sea. Tanaidacea is one of the most thread-dependent taxa in the Crustacea, constructing tubes, spun with their silk, for shelter. In this work, we sequenced and assembled the comprehensive transcriptome of 23 tanaidaceans encompassing 14 families and 4 superfamilies of Tanaidacea, and performed silk proteomics of Zeuxo ezoensis to search for its silk genes. As a result, we identified two families of silk proteins, that are conserved across the four superfamilies. The long and repetitive nature of these silk genes resembles that of other silk-producing organisms, and the two families of proteins are similar in composition to silkworm and caddisworm fibroins, respectively. Moreover, the amino acid composition of the repetitive motifs of tanaidacean silk tends to be more hydrophilic, and therefore could be a useful resource to study their unique adaptation of silk use in a marine environment. The availability of comprehensive transcriptome data in these taxa, coupled with proteomic evidence of their silk genes, will facilitate evolutionary and ecological studies.
Sample:
SAMN18530300 • SRS8629770 • All experiments • All runs
Library:
Name: R35
Instrument: NextSeq 500
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: PAIRED
Runs: 1 run, 19.4M spots, 5.8G bases, 2.6Gb
Run# of Spots# of BasesSizePublished
SRR1413586419,439,3095.8G2.6Gb2021-11-26

ID:
13948330

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