F.vescaH4x4_PoolTranscrSMART_NONnorm - SRA

SRX030797: F.vescaH4x4_PoolTranscrSMART_NONnorm
2 ILLUMINA (Illumina Genome Analyzer II) runs: 117.2M spots, 4.2G bases, 3.3Gb downloads

Design: The full-length (FL) enriched cDNA library was prepared using SMART method and MINT cDNA synthesis kit (Evrogene) as suggested by the manufacturer. The FL enriched cDNA library for the Illumina-based high throughput sequencing was prepared as described (Filichkin et al., 2009, Fox et al., 2009). Briefly, 5 µg of double-stranded cDNA in a 50 µL of TE buffer (10 mM Tris, 1 mM EDTA; pH 8.0) was mixed with 750 µL of nebulization buffer [25% (v/v) glycerol in TE buffer] and sheared for 7 min. in a nebulizer (Invitrogen) using compressed nitrogen at 36 psi. Before ligation with Illumina adapters the fragmented cDNA was purified using “QIAquick PCR Purification Kit” (Qiagen) according to the manufacturer protocol. The cDNA library was amplified for 9, 11, and 13 cycles. "

Submitted by: Oregon St Univ - Center for Genome Research & Biocomputing (OSU-CGRB)

Study: The genome of woodland strawberry (Fragaria vesca)

• SRP004287 • All experiments • All runs

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The woodland strawberry, Fragaria vesca (2n=2x=14), represents a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (206Mb), is amenable to genetic transformation, and shares substantial sequence identity with cultivated strawberry (F. × ananassa) and other economic rosaceous plants. Here we report the draft F. vesca genome, sequenced to 39x coverage using second-generation technology and de novo assembly. Anchorage to the genetic linkage map assembles the genome into seven pseudochromosomes. This diploid strawberry lacks large genome duplications shared among other rosids. Gene prediction modeling identified 34,809 genes, with most supported by transcriptome mapping. Genes critical to valuable horticultural traits including flavor, nutritional value and flowering time are identified. Macro-syntenic relationships between Fragaria and Prunus permit reconstruction of a hypothetical ancestral Rosaceae genome having nine chromosomes. Inclusion of Fragaria sequence in a phylogenetic analysis of 154 protein-coding genes suggests that Populus should be reassigned from Fabidae to Malvidae.

Sample: Fragaria vesca subsp. vesca H4x4 pooled tissues

SAMN00120059 • SRS120982 • All experiments • All runs

Organism: Fragaria vesca subsp. vesca

Library:

Name: FL_cDNA_Library

Instrument: Illumina Genome Analyzer II

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Spot descriptor:

1 forward

Runs: 2 runs, 117.2M spots, 4.2G bases, 3.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR072202	67,509,723	2.4G	1.9Gb	2010-12-15
SRR081562	49,670,279	1.8G	1.4Gb	2010-12-15

ID:: 37507

SRA

Sequence Read Archive

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