RNA expression in Vaccinium virgatum leaves, berries and buds

Overview
Analysis NameRNA expression in Vaccinium virgatum leaves, berries and buds
MethodTrinity, SOAPdenovo-Trans, TransABySS, Velvet
SourcePRJNA417702
Date performed2017-11-20

Leaves, green berries, and bud tips from Vaccinium virgatum cv. Premier were sequenced, a de novo transcriptome was assembled, and differential transcript expression levels were calculated.  The manuscript is currently in preparation and the expression data was provided to GDV pre-publication by M. Paya-Milans and M. Staton.  NCBI BioProject PRJNA417702.

Read depth per library:

Sample Read number NCBI Biomaterial accession NCBI SRA accession
Curledleaf_1 17652317 SAMN08002206 SRX3380186
Curledleaf_2 17924099 SAMN08002206 SRX3380187
GreenBerry_1 17652317 SAMN08002184 SRX3380182
GreenBerry_2 17924099 SAMN08002184 SRX3380183
PinkTipBud_1 17652317 SAMN08002000 SRX3380184
PinkTipBud_2 17924099 SAMN08002000 SRX3380185

Assembly Methods:

Two settings of k-mer 25 and k-mer 31 were applied in Trinity de novo assembly, and default settings on genome guided assembly. k-mer range of 25 to 55 with a step size of 10 were used in SOAPdenovo-Trans, TransABySS and velvet. To remove the redundancy on Trinity and SOAPdenovo-Trans, all contigs were pooled by software and clustered using CD-HIT-EST v4.6.6 with 95% identity. On velvet and TransABySS, reduced assemblies were obtained with Oases and transabyss-merge, respectively. The result of the four programs were pooled and reduced with CD-HIT to obtain the final transcriptome.

Properties
Additional information about this analysis:
Property NameValue
Analysis expression biosourceprovider id
Analysis expression arraydesign id
Analysis expression organism id121
Analysis expression associated analysis id43
Analysis expression assaydate2018-4-27 00:00:00
Analysis expression assay description
Analysis expression acquisitiondate2018-4-27 00:00:00
Analysis expression acquisition uri
Analysis expression quantificationdate2018-4-27 00:00:00
Analysis expression quantification uri
Analysis expression assay protocol id0
Analysis expression acquisition protocol id0
Analysis expression quantification protocol id0
Analysis expression assay operator id
Analysis expression quantification operator id
Analysis expression filetypemat
Analysis expression submit job0
Analysis expression fileext
Analysis expression filepath/mainlab/research/vaccinium/VaccRNAseq-FromMeg_Nov2017/Vaccinium_database/Vv_normCnt.txt
Analysis expression re start
Analysis expression re end
Analysis expression feature uniquenamesname