DOI: 10.5061/dryad.4sf33
title: Data from: Genome-wide discovery and characterization of maize long non-coding RNAs

description: Background: Long noncoding RNAs (lncRNAs) are transcripts that are 200 bp
 or longer, do not encode proteins, and potentially play important roles in
 eukaryotic gene regulation. However, the number, characteristics and
 expression inheritance pattern of lncRNAs in maize are still largely
 unknown. Results: By exploiting available public ESTs, maize whole genome
 sequence annotation and RNA-seq datasets from 30 different experiments, we
 identified 20,163 putative lncRNA. Of these lncRNAs, more than 90% are
 predicted to be the precursors of small RNAs, while 1,704 are considered
 to be high-confidence lncRNAs (HC-lncRNAs). HC-lncRNAs have an average
 transcript length of 463 bp and HC-lncRNA genes contain fewer exons than
 annotated genes (1.2 exons versus 3.5 for the Filtered Gene Set). Based on
 the expression pattern of these lncRNAs in 13 distinct tissues and 105
 maize recombinant inbred lines (RILs), more than 50% of the HC-lncRNAs are
 expressed in a tissue-specific manner, a result that is supported by
 epigenetic marks. Intriguingly, the inheritance of lncRNA expression
 patterns in 105 RILs reveals apparent transgressive segregation, and maize
 lncRNAs are less affected by cis- than by trans- genetic factors.
 Conclusions: We integrate all available transcriptomic datasets to
 identify a comprehensive set of lncRNAs, provide a unique annotation
 resource of the maize genome and a genome-wide characterization of maize
 lncRNAs, and explore the genetic control of their expression using
 expression quantitative trait locus mapping.
description: LncRNA_Finder - Pipeline
 Source CodeSource code of the
 pipeline-LncRNA_Finder THIS SOFTWARE IS PROVIDED BY THE AUTHORS AND
 CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES,
 INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
 AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL LIN
 LI, NATHAN M. SPRINGER, or GARY J. MUEHLBAUER (OR UNIVERSITY OF MINNESOTA)
 BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
 CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
 SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
 INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
 CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
 ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
 POSSIBILITY OF SUCH DAMAGE. DESCRIPTION: LncRNA_Finder enables the
 discovery of long noncoding RNAs using native sequence fasta files. This
 script essentially uses the results from external alignment programs and
 performs long noncoding RNA filtering via a set of specified parameters.
 2, Prerequisite of external softwares Need to install ncbi_blast
 standalone package, bowtie and cpc in your local environment correctly and
 set the running path of external programs at the beginning of the pipeline
 3, Usage Perl LncRNA_Finder.pl -i -p
 -k -s
 -o [-t &lt;# of thread&gt;]
 [-r ] [-f ] [-m
 &lt;# of mismatch&gt;] [-e ] Options: -i
 -p -k
 -s -o -h help -t number of thread for the computation ||
 default=4 -r minimum lncRNA length || default=200 -f
 maximum potential ORF length of lncRNAs || default=100 -m
 number of mismatch in the alignment with smallRNA || default=0
 -e E-value of the alignment against protein database ||
 default=1.0e-3LncRNA_Finder.plall_putative_lncRNAs-SequenceThe transcript sequences of all the 20,163 putative lncRNAs identified in maizeall_putative_lncRNAs.faall_putative_lncRNAs-GTFThe GTF file of all the 20,163 putative lncRNAs identified in maizeall_putative_lncRNAs.gtfpre-lncRNAs SequenceThe transcript sequences of 18,459 pre-lncRNAs identified in maizepre-lncRNAs.fapre-lncRNAs-GTFThe GTF file of 18,459 pre-lncRNAs identified in maizepre-lncRNAs.gtfHigh Confidence lncRNAs-SequenceThe transcript sequences of 1,704 High Confidence lncRNAs identified in maizeHC-lncRNAs.faHigh Confidence lncRNAs-GTFThe GTF file of 1,704 High Confidence lncRNAs in maizeHC-lncRNAs.gtfSummary of datasets we've usedTranscribed sequences from the maize reference inbred line-B73 were collected from the Sequence Read Archive and GenBank. Data available in the Sequence Read Archive from the maize inbred line B73 included 30 RNA-seq experiments from 13 distinct tissues (leaf, immature ear, immature tassel, seed, endosperm, embryo, embryo sac, anther, ovule, pollen, silk, and root and shoot apical meristem) encompassing a total of 1.168 billion reads with read lengths ranging from 35 to 110 nucleotides. Maize ESTs from a vast variety of tissues and stages were also collected from GenBank and integrated with the maize B73 genome annotation (AGP v2).Datasets_Info.xls