RNA expression in Vaccinium virgatum leaves, berries and buds

Analysis NameRNA expression in Vaccinium virgatum leaves, berries and buds
MethodTrinity, SOAPdenovo-Trans, TransABySS, Velvet
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.

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
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Analysis expression filepath/mainlab/research/vaccinium/VaccRNAseq-FromMeg_Nov2017/Vaccinium_database/Vv_normCnt.txt
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Analysis expression re end
Analysis expression feature uniquenamesname