HuLnc Field2018 bb Track Settings
 
Human lncRNA from Field et al 2018

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Data schema/format description and download
Assembly: Chimp Feb. 2011 (CSAC 2.1.4/panTro4)
Data last updated at UCSC: 2018-11-05 09:59:48

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.