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Title: Next Generation Sequencing facilitates analysis of gene expression from Rehmannia glutinosa associated with replanting disease      
dateReleased:
12-31-2015
description:
Purpose: the technology of Solexa/Illumina (RNA-seq) is an attractive alternative to the transcriptome sequencing. The goals of this study are to investigate transcriptional changes in replanted R. glutinosa leaves and identify genes responding to the disease. Methods:Totally 6.01and 6.15 million raw tags were measured from leaves of the first year planted (L1) and the second year replanted R. glutinosa (L2) at the tuberous root expansion stage, respectively. mRNA profiles of leaves of the first year planted (L1) and the second year replanted R. glutinosa (L2) at the tuberous root expansion stage, were generated by deep sequencing (Illumina HiSeq™ 2000 system). qRT–PCR validation was performed using SYBR Green assays. Results: we obtained a total of 6.01 and 6.15 million total tags including 377,200 and 361,659 distinct tags from the L1 and L2 samples, respectively. Removal of low quality tags, 161,298 and 149,290 distinct clean tags were remained.With reference to the 94,544 non-redundant consensus sequences defined by the RNA-seq transcriptomic procedure, 60,574 genes had the diagnostic CATG site, which were taken as reference distinct sequences for DGE analysis. 47,458 of the L1 tag library and 42,247 of the L2 tag library were perfectly matched the reference sequences. we screened differentially expressed genes in the L1 and L2 libraries by digital gene expression (DGE) technique. Finally, a set of 1,954 genes may be in differential expression of L2. By bioinformatics and qRT-PCR, the 117 most strongly differentially expressed ones were considered to be prime candidates for responsible for replanting disease. Conclusions: The study provides an important resource for further investigating the cause of replanting disease and developing the methods to control or subtract its injury. Leaf mRNA profiles of L1 (The first year planted R. glutinosa leaves ) and L2 (the second year replanted R. glutinosa leaves) root expansion stage were generated by deep sequencing (using Illumina HiSeq™ 2000 system)
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-54620
refinement:
raw
alternateIdentifiers:
54620
keywords:
functional genomics
dateModified:
01-02-2016
availability:
available
types:
gene expression
name:
Rehmannia glutinosa
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-54620/E-GEOD-54620.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-54620/E-GEOD-54620.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE54620
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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