Description
These tracks represent locus annotations in four primate species for lncRNAs expressed during
early cortical development as described in Field et al., 2018. Briefly, block loci were generated
for Cufflinks (Trapnell et al., 2012) generated transcript model predictions if they were within
10kb, originating from the same strand, co-expressed at our differentiation assay time points,
and uninterrupted by antisense transcription or annotated protein-coding gene models. The data
sets used to generate these locus models are available on GEO (GSE106245).
Each track shows lncRNA gene loci. For the non-human primates each locus number
corresponds to the locus in hg19, determined as described in the Methods section below.
- human: hg19
- chimpanzee: panTro4
- orangutan: ponAbe2
- rhesus macaque: rheMac8
Display Conventions and Configuration
For non-human primates, locus names refer to human.
Item Search By Locus Name
It is possible to use the genome browser search box to jump to the locus of any item. The locus
names (in any of the primate assemblies) are of the form "HuLncNNN", where NNN is the
locus number. This form is case sensitive. For example, you can type "HuLnc108" in the
search box and click "go" and the browser will jump to the location of the HuLnc108 locus.
Note that the TrEx loci referred to in the publication are a subset of these loci, but use the HuLnc
name. So the above search is used to find TrEx108.
Methods
The full description of selection of transcripts for the human hg19 gene model,
and the derivation of associated transcripts in the other primates can be found in Field AR, et
al., 2018. Here is a brief synopsis.
Cufflinks v2.0.2 suite (Trapnell et al., 2012) was used to assemble transcript predictions of
potentially unannotated lncRNAs from human cortical neuron differentiation time points and the
Cuffmerge tool was used to combine these annotations with FANTOM5 transcripts. Guided by
this Cufflinks annotation set in human each lncRNA transcript was assigned a putative gene
locus with a lncRNA ID number based on overlap with block loci defined by co-expression of
transcripts within 10kb at at least one time time point, expression from the same strand,
uninterrupted by antisense transcription, and no overlap with known protein-coding genes. The
equivalent locus in each other primate genome was generated by the liftOver tool in the UCSC
Genome Browser. The RNA-seq data sets used to generate these locus models are available
on GEO (GSE106245).
Data were generated and processed at the UC Santa Cruz Genomics Institute. For inquiries,
please contact us at the following address:
ssalama@ucsc.
edu
References
Field AR, Jacobs FMJ, Fiddes IT, Phillips APR, Reyes-Ortiz AM, LaMontagne E, Whitehead L,
Meng V, Rosenkrantz JL, Olsen M, Hauessler M, Katzman S, Salama SR, Haussler D.
Structurally conserved primate lncRNAs are transiently expressed during human cortical
differentiation and influence cell type specific genes. Stem Cell Reports. 2018. (In Press).
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL,
and Pachter, L. (2012). Differential gene and transcript expression analysis of RNA-seq
experiments with TopHat and Cufflinks. Nature Protocols 7(3), 562-578.
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