Mountain View
biomedical and healthCAre Data Discovery Index Ecosystem
help Advanced Search
Title: Transcription profiling by high throughput sequencing of drought-treated and well-watered fertilized ovary and basal leaf meristem tissue in maize      
dateReleased:
08-14-2012
description:
Purpose: To study the effects of drought at the transcriptomic level on two different actively dividing maize tissue: the ovaries, and the leaf meristem Methods: The Illumina reads were mapped to the maize B73 reference genome using Tophat followed by transcriptome reconstruction using Cufflinks. The FPKM valuse were extracted from cufflinks output and an R package called Limma was used to identify differentially expressed genes under drought under both tissues Results and Conclusions: Different processes which were differentially expressed under drought in both tissues were identified and analyzed in detail. A working hypothesis was formulated to account for the observed susceptibility of the reproductive tissue when compared to the robust response of the vegetative tissue. This analysis also servers as a basis for future study on drought-induced embryo abortion. Maize (Zea mays) plants of inbred line B73 were grown in the green house under well watered and drought stress conditions until they reached the reproductive stage (at the onset of silk emergence). For the drought stress two to three days after irrigation was withheld, the plants were hand pollinated, and 24 hours after pollination measurements and samples were collected for transcriptome analysis. At the end of the drought period (1DAP) the basal leaf meristem of the three youngest leaves and the ovary tissues were sampled for Illumina deep sequencing. Samples were labeled as well watered control leaf meristem (MLC), well watered control ovaries/ "cob" (MCC), drought stressed leaf meristem (MLD) and drought stressed ovary tissue (MCD). There are 8 libraries in total including one biological replicate for each condition.
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-40070
refinement:
raw
alternateIdentifiers:
40070
keywords:
functional genomics
dateModified:
03-09-2016
availability:
available
types:
gene expression
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-40070/E-GEOD-40070.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-40070/E-GEOD-40070.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=GSE40070
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

Feedback?

If you are having problems using our tools, or if you would just like to send us some feedback, please post your questions on GitHub.