qTeller MaizeGDB
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September 2018: MaizeGDB qTeller has a new look! A navigation bar at the top with tool drop-down menus makes navigation easier.

27-August-2018: The issue with qTeller due to a server problem has been resolved.

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Methods

All RNA-seq reads were mapped using the STAR 2.5.3 aligner, default settings, and FPKM abundances were counted using Cufflinks 2.2.1, default settings. Fastq reads were not trimmed except for the Walley RNA-seq data, which was mapped by Jesse Walsh of MaizeGDB. Reads with multiple bioreps were merged and averaged after the FPKM abundance Cufflinks step. Error bars in bar charts denote the "Low" and "High" FPKMs for each sample.


Metadata

To download a list of all RNA-seq runs, their SRR IDs, and other information, click HERE.


Dataset sources and authors/labs

The following papers [by lab] were the sources of the RNA-seq datasets included in these qTeller datasets (sources link to publications):

B73 v4:

Forestan 2016 [Varotto Lab]
Johnston 2014 [Scanlon Lab]
Kakumanu 2012 [Pereira Lab]
Maize Atlas Stelpflug 2015 [Kaeppler Lab]
Walley 2016 [Briggs Lab]
Waters 2017 [Springer Lab]