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Brain RNA-seq specifications


Unique identifier OMICS_06097
Name Brain RNA-seq
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes


  • Rodents
    • Mus musculus


  • person_outline Qingyun Li

Additional information

Publications for Brain RNA-seq

Brain RNA-seq citations


Identification and characterization of functional modules reflecting transcriptome transition during human neuron maturation

BMC Genomics
PMCID: 5905132
PMID: 29665773
DOI: 10.1186/s12864-018-4649-2

[…] ported that neuron maturation explains the majority of brain transcriptome changes during prenatal and new-born postnatal development []. Therefore, we took the advantage of fetal and early postnatal brain RNA-seq dataset in BrainSpan and another age series RNA-seq data [], to compare the brain transcriptome before and after postnatal day 100. Remarkably, 28 out of the 33 discriminating modules sh […]


Accurate identification of RNA editing sites from primitive sequence with deep neural networks

Sci Rep
PMCID: 5902551
PMID: 29662087
DOI: 10.1038/s41598-018-24298-y

[…] are RNA editing sites identified by different laboratories, regardless of other factors.Besides, we investigated the impact of sequence depth on RNA editing site identification by down sampling human brain RNA-seq data of 16 individuals from the SEQC project (Table ). As sequencing depth increased, the number of RNA editing sites stably increased. Notably, the A-to-I ratio increased with sequence […]


Highly conserved molecular pathways, including Wnt signaling, promote functional recovery from spinal cord injury in lampreys

Sci Rep
PMCID: 5768751
PMID: 29335507
DOI: 10.1038/s41598-017-18757-1
call_split See protocol

[…] number of RNA-Seq reads per timepoint was 135,742,182 in spinal cord and 139,024,579 in brain. Total RNA-Seq reads for all time points was 1,493,164,006 for the spinal cord and 1,529,270,374 for the brain. RNA-Seq reads were mapped against gene models from the publicly available lamprey genome (Ensembl; Pmarinus_7.0). Gene expression levels were estimated for all lamprey gene models separately fo […]


Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability

Genome Med
PMCID: 5518101
PMID: 28724449
DOI: 10.1186/s13073-017-0452-y

[…] onal role of the two new functional elements described in this work (see “”). The pipeline consists of two main steps: de novo transcriptome assembly and gene/isoform detection. We investigated fetal brain RNA-Seq paired-end data (hg19) and collected BAM alignment files for six experiments (ENCODE ENCSR000AEW, ENCSR000AFD, ENCSR000AFE, ENCSR000AEX, ENCSR000AEY, ENCSR000AFJ; see Additional file : T […]


Comprehensive investigation of temporal and autism associated cell type composition dependent and independent gene expression changes in human brains

Sci Rep
PMCID: 5482876
PMID: 28646201
DOI: 10.1038/s41598-017-04356-7

[…] by DR, while CIBERSORT performed better than QP (Supplementary Figure ).In addition to the postnatal brain transcriptome, we further applied the three algorithms to the human embryonic developmental brain RNA-seq data obtained from BrainSpan database (Fig.  and Supplementary Figure ). DR-estimated composition pattern successfully recapitulated the domination of replicating neurons dominate before […]


Huntington’s disease blood and brain show a common gene expression pattern and share an immune signature with Alzheimer’s disease

Sci Rep
PMCID: 5359597
PMID: 28322270
DOI: 10.1038/srep44849

[…] he most significantly dysregulated modules in caudate nucleus, the most prominently affected region in HD brain. This suggests mutant huntingtin drives a common pathogenic signature in both blood and brain.RNA-Seq more comprehensively and accurately quantifies mRNA than hybridisation-based microarrays or tag-based methods. Expression of phosphatidylcholine transfer protein (PCTP) significantly cor […]


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Brain RNA-seq institution(s)
Department of Neurobiology, Stanford University School of Medicine, Stanford, CA, USA; Bradley Department of Electrical and Computer Engineering, Virginia Polytechnic Institute and State University, Arlington, VA, USA; Departments of Bioengineering and Applied Physics, Stanford University and Chan Zuckerberg Biohub, Stanford, CA, USA; Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA; Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Stanford, CA, USA
Brain RNA-seq funding source(s)
Supported the JPB Foundation, Adelson Medical Research Foundation, Vincent J. Coates Foundation, National Institutes of Health (R01 DA015043), the Veterans Administration, the NOMIS Foundation, National Institutes of Health (R01 MH110504), the Helen Hay Whitney Foundation, National Multiple Sclerosis Society, the Life Science Research Foundation, and by a Stanford Medicine Dean’s Fellowship.

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