Silene undulata - SRA

SRX2070459: Silene undulata
1 ILLUMINA (Illumina HiSeq 2500) run: 33M spots, 8.3G bases, 2.8Gb downloads

Design: To develop new transcriptomic resources for Silene, we collected seeds and/or leaf tissue from S. grisebachii, S. sartorii, and S. subconica in Greece during Summer 2015 (Fig. 1;Table S1). For S. subconica, 4-5 rosette leaves were preserved in RNAlater from a single individual and frozen at -20 °C for ~1 week prior to transport to Colorado State University, where they were frozen at -80 °C for ~4 months prior to RNA extraction via an RNeasy Plant Mini Kit (Qiagen). For S. sartorii and S. grisebachii, seeds were collected from mature fruit in Greece and germinated on soil in June 2015 (Fafard 2SV mix supplemented with vermiculite and perlite) and grown under a 16-hr/8-hr light/dark cycle with regular watering and fertilizer treatments in greenhouse facilities at Colorado State University. After growing for 5 months, RNA was extracted from 4-5 rosette leaves from a single individual of each species as described above. Seeds were also obtained for S. ammophila, S. conoidea, and S. undulata (Fig. 1; Table S1), with growing conditions and RNA extractions for these species as described above. Resulting RNA was sent to the Yale Center for Genome Analysis for cDNA library preparation and Illumina sequencing. A Ribo-Zero Plant Leaf rRNA Removal Kit (Illumina) was used during library preparation in order to capture organellar transcripts, which are not poly-adenylated, for future studies. The resulting six strand-specific cDNA libraries were then sequenced on a single Illumina HiSeq 2500 lane. Paired-end, 151 bp reads were delivered in FASTQ format and are available via the sequence read archive (SRA) at the National Center for Biotechnology Information (NCBI) (Table S2). Reads were used as delivered (i.e., no quality filtering was performed) to assemble strand-specific transcriptomes de novo for each species using Trinity r20140717 (GRABHERR et al. 2011), with default parameters and in silico normalization of reads. Resulting contigs were deposited in NCBI’s transcriptome shotgun assembly (TSA) database (Table S2).

Submitted by: Colorado State University

Study: Transcriptomic resources for Silene ammophila, S. conoidea, S. griesbachii, S. sartorii, S. subconica, and S. undulata

PRJNA341271 • SRP083905 • All experiments • All runs

show Abstracthide Abstract

Transcriptomic resources were developed from six species of Silene (Silene ammophila, S. conoidea, S. griesbachii, S. sartorii, S. subconica, and S. undulata) with fast-evolving mtDNA in order to investigate genomics and mitonuclear interactions within this group.

Sample: Silene undulata leaf transcriptome

SAMN05717981 • SRS1661057 • All experiments • All runs

Organism: Silene undulata

Library:

Name: Cope

Instrument: Illumina HiSeq 2500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Runs: 1 run, 33M spots, 8.3G bases, 2.8Gb

Run	# of Spots	# of Bases	Size	Published
SRR4105784	33,041,498	8.3G	2.8Gb	2016-09-05

ID:: 3064712

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Sequence Read Archive

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