Evidence map›Paper›PMID 25243066›Full record

ArticleGigaScience2014

De novo assembly of the common marmoset transcriptome from NextGen mRNA sequences.

Mnirnal D Maudhoo, Dongren Ren, Julien S Gradnigo, Robert M Gibbs, Austin C Lubker, Etsuko N Moriyama, Jeffrey A French, Robert B Norgren

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in GigaScience, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

  1. Review
  2. Transcriptome of the Southern MuriquiFrontiers in genetics · 2020
    Article
  3. Review
  4. Article
  5. Article
  6. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Mnirnal D MaudhooDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
Dongren RenCallitrichid Research Center, Department of Psychology, University of Nebraska, Omaha, USA ; Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang 330045, China.
Julien S GradnigoSchool of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, 403 Manter Hall, Lincoln, Nebraska 68588-0118, USA.
Robert M GibbsDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
Austin C LubkerDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.
Etsuko N MoriyamaSchool of Biological Sciences & Center for Plant Science Innovation, University of Nebraska-Lincoln, 403 Manter Hall, Lincoln, Nebraska 68588-0118, USA.
Jeffrey A FrenchCallitrichid Research Center, Department of Psychology, University of Nebraska, Omaha, USA.
Robert B NorgrenDepartment of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska 68198, USA.

Funding

Parenting, Sibling-Support, and Infant DevelopmentR01HD042882 · NICHD · UNIVERSITY OF NEBRASKA OMAHA · PI FRENCH, JEFFREY A · 2002 to 2014
$1.7M
NICHD NIH HHS R01 HD042882
6 · The paper itself

Abstract

backgroundNonhuman 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, including both raw sequences and assembled transcripts, will aid in the annotation of the newly released marmoset assembly.

findingsRNA WAS EXTRACTED FROM FIVE TISSUES: skeletal muscle, bladder and hippocampus from a male common marmoset, and cerebral cortex and cerebellum from a female common marmoset. All five RNA samples were sequenced on the Illumina HiSeq 2000 platform. Sequences were deposited in the NCBI Sequence Read Archive. Transcripts were assembled, annotated and deposited in the NCBI Transcriptome Shotgun Assembly database.

conclusionsWe have provided a high quality annotation of 51,163 transcripts with full-length coding sequence. This set represented a total of 10,833 unique genes. In addition to providing empirical support for the existence of these 10,833 genes, we also provide sequence information for 2,422 genes that were not previously identified in the Ensembl annotation of the marmoset genome.

Indexed as

AssemblyCallithrix jacchusCommon marmosetmRNA-seqTranscriptome

Identifiers

PMID25243066
PMCPMC4169894

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.