Trebouxia jamesii 454 amplicon sequences - SRA

SRX1967739: Trebouxia jamesii 454 amplicon sequences
1 LS454 (454 GS Junior) run: 6,932 spots, 3.1M bases, 6.7Mb downloads

Design: We performed a DNA extraction from the Trebouxia jamesii culture and a RT-PCR and a PCR using the nr-SSU-1780/5.8S 2R primers. The number of cycles of PCR were determined by the average Ct of the RT-PCR and the fusion primers designed following the GS Junior System Guidelines for Amplicon Experimental Design (Roche, Branford, USA) were used, selecting the unidirectional sequencing protocol for library construction (Lib-L chemistry for emulsion PCR, emPCR, ‘One-Way Reads’. The forward fusion primer was: 5'-A-KEY- nr-SSU-1780–3' and the reverse fusion primer was: 5’-B-KEY-MID-5.8S-2R-3’, where A and B represent the pyrosequencing adaptors, and the multiplex identifier (MID) was added for post-sequencing sample identification.

Submitted by: UNIVERSIDAD DE VALENCIA

Study: Ramalina farinacea Metagenome

PRJNA330765 • SRP079117 • All experiments • All runs

show Abstracthide Abstract

This work establishes, to our knowledge, the first attempt to apply pyrosequencing techniques to analyze lichen-symbiotic microalgae communities in depth on the lichen Ramalina farinacea using high-throughput 454 pyrosequencing with algal-specific primers targeting the ITS region.

Sample: Amplicon sequences from Trebouxia jamesii

SAMN05425718 • SRS1577132 • All experiments • All runs

Organism: Trebouxia jamesii

Library:

Name: Trebouxia jamesii

Instrument: 454 GS Junior

Strategy: AMPLICON

Source: GENOMIC

Selection: PCR

Layout: SINGLE

Spot descriptor:

5 forward

Pipeline: show...hide...

Program	Version
sfffile
sff_extract
Trim_Edges	seq_crumbs-0.1.8
BLASTCLUST	2.2.26
MUSCLE	v3.8.31

Runs: 1 run, 6,932 spots, 3.1M bases, 6.7Mb

Run	# of Spots	# of Bases	Size	Published
SRR3938470	6,932	3.1M	6.7Mb	2017-07-21

ID:: 2831373

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