March 2021: MaizeGDB qTeller now has data for version 5 of B73 and the NAM Founders! Select either "B73v5 [NAM Consortium]" or "NAM Founders [NAM Consortium]" under the drop-down menus above.

October 2019: MaizeGDB qTeller has a new look! Now we can compare expression and abundance under the menu 'Compare RNA & Protein'.

Questions or suggestions? Please let us know on the Contact page.

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.

The qTeller web pages are organized based on the project from which the RNA-seq data was collected, processed, and sequenced. This ensures that all the data within a collection has been extracted and sequenced the same way, so as to avoid the issue of artifactual relative abundances due to differences in laboratory technique or environment. However, two caveats must be noted:

1) Abundances across different datasets/laboratories may differ somewhat due to differences in laboratory handling and other factors.

2) Cross-genome RNA-seq datasets (such as for the NAM Founders datasets) contain FPKM values normalized within each genome, rather than across genomes.

To confirm comparative RNA-seq results in qTeller observed across genomes or datasets, researchers can use differential gene expression software such as EdgeR with the mapped bam files below.

Reads data used in qTeller

BAM files used as inputs for MaizeGDB qTeller to generate FPKM values:

B73v5 mapped bam files:

irods download link: /iplant/home/maizegdb/maizegdb/B73v5_JBROWSE_AND_ANALYSES/B73v5_RNA-seq

NAM Founder mapped bam files:

irods download link: /iplant/home/maizegdb/maizegdb/NAM_PROJECT_JBROWSE_AND_ANALYSES/NAM_RNA-seq

FPKM abundance values used in MaizeGDB qTeller:

B73v4 FPKM abundance values:

irods download link: /iplant/home/maizegdb/maizegdb/MaizeGDB_qTeller_FPKM/B73v4_qTeller_FPKM
Web download link: https://datacommons.cyverse.org/browse/iplant/home/maizegdb/maizegdb/MaizeGDB_qTeller_FPKM/B73v4_qTeller_FPKM

B73v5 FPKM abundance values:

irods download link: /iplant/home/maizegdb/maizegdb/MaizeGDB_qTeller_FPKM/B73v5_qTeller_FPKM
Web download link: https://datacommons.cyverse.org/browse/iplant/home/maizegdb/maizegdb/MaizeGDB_qTeller_FPKM/B73v5_qTeller_FPKM

NAM Founder FPKM abundance values:

irods download link: /iplant/home/maizegdb/maizegdb/MaizeGDB_qTeller_FPKM/NAM_qTeller_FPKM
Web download link: https://datacommons.cyverse.org/browse/iplant/home/maizegdb/maizegdb/MaizeGDB_qTeller_FPKM/NAM_qTeller_FPKM

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):

Single Genome, B73v4:

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

Single Genome, B73v5:

Forestan 2016 [Varotto Lab]
Johnston 2014 [Scanlon Lab]
Kakumanu 2012 [Pereira Lab]
Maize Atlas Stelpflug 2015 [Kaeppler Lab]
Makarevitch 2015 [Springer Lab]
Opitz 2014 [Hochholdinger Lab]
Walley 2016 [Briggs Lab]
Warman 2020 [Fowler Lab]
Chen 2017 [Dresselhaus lab]

Multiple Genomes:

NAM Consortium
Diepenbrock 2017 [DellaPenna Lab]
Lin 2017 [Schnable Lab]

Protein Abudances, B73v4:

Walley 2019 [Briggs Lab]

Protein Abudances, B73v5:

Walley 2019 [Briggs Lab]