Malacobdella grossa transcriptome - SRA

SRX731465: Malacobdella grossa transcriptome
1 ILLUMINA (Illumina HiSeq 2000) run: 15.3M spots, 3.1G bases, 2Gb downloads

Design: Specimens were preserved in RNAlater overnight at room temperature or 4°C followed by storage at ‑80°C or fresh tissue was frozen at -80°C. Total RNA was extracted using the RNAqueous Micro kit (Ambion) without a DNase digestion, the RNeasy Micro kit (Qiagen) with on-column DNase digestion, or TRIzol (Invitrogen) followed by purification using the RNeasy kit (Qiagen) with on-column DNase digestion. RNA concentration was estimated using a NanoDrop 2000 (Thermo Scientific) and RNA quality was evaluated on a 1% SB agarose gel. For most libraries, first-strand cDNA was synthesized from 1 µg of total RNA. However, for some very small samples, the eluted RNA was too dilute to measure using the NanoDrop or visualize with agaorse gel electrophoresis. In cases where less than 1 µg of total RNA was available, 1 µl of RNase-OUT (Invitrogen) was mixed with all of the eluted RNA, this mixture was vacuum-centrifuged to a volume of 3 µl, and all 3 µl were used to make cDNA. First-strand cDNA synthesis was performed using the SMART cDNA library construction kit (Clontech) as per the manufacturer’s instructions except that the provided 3’ oligo was replaced with the Cap-Trsa-CV oligo as per Meyer et al. (2009). Full-length cDNA was then amplified using the Advantage 2 PCR system (Clontech) using the minimum number of PCR cycles possible (usually 17-19) and sent to the HudsonAlpha Institute for Biotechnology (Huntsville, AL, USA) for paired-end (PE) library preparation and Illumina sequencing. Each library was sequenced using approximately one-sixth of an Illumina HiSeq 2000 lane using the 2 X 100 bp PE chemistry.

Submitted by: The University of Queensland

Study: Repurposed transcriptomes facilitate discovery of innate immunity Toll-Like Receptor (TRLs) genes across Lophotrochozoa

PRJNA263418 • SRP048758 • All experiments • All runs

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The growing volume of genomic data from across life represents opportunities for deriving valuable biological information from data that was initially collected for another purpose. Here, we use transcriptomes collected for phylogenomic studies to search for Toll-Like Receptor (TRL) genes in poorly sampled lophotrochozoan clades (Annelida, Mollusca, Brachiopoda, Phoronida, and Entoprocta) and one ecdysozoan clade (Priapula). TRL genes are involved in innate immunity across animals by recognizing potential microbial infection. They have an extracellular Leucine-Rich Repeat (LRR) domain connected to transmembrane and intracellular Toll/Interleukin-1 Receptor (TIR) domains. As such, these genes are important in initiating a signaling pathway to initiate defense. We found at least one TRL ortholog in all taxa examined suggesting all these taxa may have innate immune systems similar to those observed in vertebrates and arthropods. Comparison to the SMART database to confirmed the presence of both the LRR and the TIR protein motifs characteristic of TRL genes. Because we looked at only one transcriptome per species, the discovery of TRL genes was limited for most taxa. However, several where found in phoronids which vary in the placement and number of LRR domains. Additionally several of the LRR containing genes were discovered, some likely involved in innate immunity.

Sample: Malacobdella grossa transcriptome

SAMN03098849 • SRS720570 • All experiments • All runs

Organism: Malacobdella grossa

Library:

Name: Malacobdella grossa transcriptome

Instrument: Illumina HiSeq 2000

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: PolyA

Layout: PAIRED

Spot descriptor:

1 forward101 reverse

Runs: 1 run, 15.3M spots, 3.1G bases, 2Gb

Run	# of Spots	# of Bases	Size	Published
SRR1611560	15,269,429	3.1G	2Gb	2014-11-21

ID:: 1057576

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