|
|
Overview
| Analysis Name | Expression: Vaccinium virgatum leaves, berries and buds |
|---|
| Method | Trinity, SOAPdenovo-Trans, TransABySS, Velvet |
|---|
| Source | PRJNA417702 |
|---|
| Date performed | 2017-11-20 |
|---|
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. Expression values are in normalized counts.
| Sample |
Tissue |
| Curledleaf_1 |
Curled leaf |
| Curledleaf_2 |
Curled leaf |
| GreenBerry_1 |
Green berry |
| GreenBerry_2 |
Green berry |
| PinkTipBud_1 |
Pink tip bud |
| PinkTipBud_2 |
Pink tip bud |
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 Name | Value |
|---|
| Analysis expression biosourceprovider id | |
| Analysis expression arraydesign id | |
| Analysis expression organism id | 121 |
| Analysis expression associated analysis id | 43 |
| Analysis expression assaydate | 2018-4-27 00:00:00 |
| Analysis expression assay description | |
| Analysis expression acquisitiondate | 2018-4-27 00:00:00 |
| Analysis expression acquisition uri | |
| Analysis expression quantificationdate | 2018-4-27 00:00:00 |
| Analysis expression quantification uri | |
| Analysis expression assay protocol id | 0 |
| Analysis expression acquisition protocol id | 0 |
| Analysis expression quantification protocol id | 0 |
| Analysis expression assay operator id | |
| Analysis expression quantification operator id | |
| Analysis expression filetype | mat |
| Analysis expression submit job | 0 |
| 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 uniquenames | name |
|
