Description

These tracks represent gene models in four primate species as described in Field, et al. 2018. Annotations were created using Cufflinks (Trapnell et al., 2012) based on RNA-seq data from weekly time points of cortical organoid differentiation in human, chimpanzee, orangutan, and rhesus macaque with FANTOM5 (Hon et al., 2017) as a reference. For the non-human primates a transmapped version of the human FANTOM5 transcripts were used as a reference in each respective species. The transcript models as well as the RNA-seq data used to produce them are available on GEO (GSE106245).

Each track shows all the transcripts in the gene model. For the non-human primates each transcript corresponds to a transcript in the the hg19 gene model, 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, transcript names refer to human.

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, et al. 2018. Here is a brief synopsis.

A progressive Cactus (Paten et al., 2011) whole genome alignment was generated between the human hg19 assembly, chimpanzee panTro4 assembly, orangutan ponAbe2 assembly, and rhesus macaque rheMac8 assembly. This alignment was used as input for CAT (https://github.com/ComparativeGenomicsToolkit/Comparative-Annotation-Toolkit, Fiddes et al., 2018) along with the FANTOM5 (Hon et al., 2017) lv3 annotation set. RNA-seq obtained from SRA (https://www.ncbi.nlm.nih.gov/sra) were used to help guide the annotation process. Cufflinks v2.0.2 suite (Trapnell et al., 2012) was used to assemble transcript predictions of potentially unannotated lncRNAs in each species and the Cuffmerge tool was used to combine these annotations with FANTOM5 transcripts. These modified and filtered FANTOM transcript models, as well as the RNA-seq data sets used to generate them, 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)

Hon, C., Ramilowski, J.A., Harshbarger, J., Bertin, N., Rackham, O.J., Gough, J., Denisenko, E., Schmeier, S., Poulsen, T.M., Severin, J., et al. (2017). An atlas of human long non-coding RNAs with accurate 5' ends. Nature 543, 199-204.

Paten, B., Earl, D., Nguyen, N., Diekhans, M., Zerbino, D., and Haussler, D. (2011). Cactus: algorithms for genome multiple sequence alignment. Genome Res 21, 1512-1528.

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.