Supporting materials for the "De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences".

Dataset type: Transcriptomic
Data released on September 04, 2014

Maudhoo MD; Ren D; Gradnigo JS; Gibbs RM; Lubker AC; Moriyama EN; French JA; Norgren RB (2014): Supporting materials for the "De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences". GigaScience Database. http://dx.doi.org/10.5524/100103

DOI10.5524/100103

Nonhuman primates are important for both biomedical studies and understanding human evolution. Although research in these areas has mostly focused on Old World primates, such as the rhesus macaque; the common marmoset (Callithrix jacchus), a New World primate, offers important advantages in comparison to other primates, such as an accelerated lifespan. To conduct Next Generation expression studies or to study primate evolution, a high quality annotation of the marmoset genome is required. The availability of marmoset transcriptome data from five tissues (skeletal muscle, bladder, hippocampus, cerebral cortex and cerebellum) including both raw sequences (after filtering low quality reads by BLAST against human RefSeq 57) and assembled transcripts, will aid in the annotation of the newly released marmoset genome assembly. Sequences were deposited in the NCBI Sequence Read Archive (PRJNA203643). Transcripts were assembled, annotated and deposited in the NCBI Transcriptome Shotgun Assembly database (5 Marmoset transcriptomes).
Here we provide the ISA-tab metadata for the entire experiment include sample metadata and links to archived data. In addition we provide the BLASTx (against RefSeq57) results in tabular format for each of the assembled transcriptomes which provides the evidence for the annotations assigned to each transcript.

Additional details

Read the peer-reviewed publication(s):

Maudhoo, M. D., Ren, D., Gradnigo, J. S., Gibbs, R. M., Lubker, A. C., Moriyama, E. N., … Norgren, R. B. (2014). De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences. GigaScience, 3(1). doi:10.1186/2047-217x-3-14





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
2218_bladder9483common marmosetwhite-tufted-ear marmosetCallithrix jacchus Age:2
Alternative accession-BioSample:SAMN02147225
Disease status:DOID:77:gastrointestinal system dis...
...
+
2218_hippocampus9483common marmosetwhite-tufted-ear marmosetCallithrix jacchus Age:2
Alternative accession-BioSample:SAMN02147224
Disease status:DOID:77:gastrointestinal system dis...
...
+
2218_skeletal_muscle9483common marmosetwhite-tufted-ear marmosetCallithrix jacchus Age:2
Alternative accession-BioSample:SAMN02147223
Disease status:DOID:77:gastrointestinal system dis...
...
+
2219_cerebellum9483common marmosetwhite-tufted-ear marmosetCallithrix jacchus Age:2
Alternative accession-BioSample:SAMN02147222
Disease status:DOID:77:gastrointestinal system dis...
...
+
2219_cerebral_cortex9483common marmosetwhite-tufted-ear marmosetCallithrix jacchus Age:2
Alternative accession-BioSample:SAMN02147221
Disease status:DOID:77:gastrointestinal system dis...
...
+
Displaying 1-5 of 5 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
2218_bladderBLASTTEXT31.07 MB2014-09-03
2219_cerebral_cortexBLASTTEXT35.79 MB2014-09-03
2219_cerebellumBLASTTEXT33.92 MB2014-09-03
2218_hippocampusBLASTTEXT31.07 MB2014-09-03
ReadmeTEXT0.5 KB2014-09-03
2218_skeletal_muscleBLASTTEXT23.62 MB2014-09-03
Displaying 1-6 of 6 File(s).
Date Action
October 19, 2015 File ISA_Marmoset_RNASeq.zip updated
October 19, 2015 File readme.txt updated
October 19, 2015 File Hippocampus.tsv updated
October 19, 2015 File Hippocampus.tsv updated
October 19, 2015 File CerebralCortex.tsv updated
October 19, 2015 File Bladder.tsv updated
October 19, 2015 File SkMuscle.tsv updated
October 19, 2015 File SkMuscle.tsv updated