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TranscriptomicsSRA of transcriptome of Hevea brasiliensis
We first report the use of next-generation massively parallel sequencing technologies and de novo transcriptome assembly to gain insight into the wide range of transcriptome of Hevea brasiliensis. The output of sequenced data showed that more than 12 million sequence reads with average length of 90n...
ORGANISM(S): Hevea brasiliensis 
2011-09-01 | E-GEOD-26514 | biostudies-arrayexpress
TranscriptomicsLong non-coding RNAs in B cells (RNA-Seq)
Using RNA sequencing and de novo transcript assembly, we identified 4516 lncRNAs expressed in 8 different stages of B cell development and activation. Chromatin immuno-precipitation sequencing was used to classify a substantial fraction (38%) of these lncRNAs as enhancer-associated or promoter-assoc...
ORGANISM(S): Mus musculus 
2016-07-15 | E-GEOD-72018 | biostudies-arrayexpress
TranscriptomicsAnalysis of porcine adipose tissue transcriptome reveals differences in de novo fatty acid synthesis in pigs with divergent muscle fatty acid composition
In pigs, adipose tissue is one of the principal organs involved in the regulation of lipid metabolism. It is particulary involved in the overall fatty acid synthesis with consequences in other lipid-target organs such as muscles and the liver. With this in mind, we have used massive, parallel high-t...
ORGANISM(S): Sus scrofa 
2014-03-31 | E-GEOD-52012 | biostudies-arrayexpress
TranscriptomicsLong non-coding RNAs display higher natural expression variability than protein-coding genes in healthy humans
Background: Long non-coding RNAs (lncRNAs) are increasingly implicated as gene regulators and may ultimately be more numerous than protein-coding genes in the human genome. Despite large numbers of reported lncRNAs, reference annotations are likely incomplete due to their lower and tighter tissue-sp...
ORGANISM(S): Homo sapiens 
2016-01-05 | E-GEOD-70390 | biostudies-arrayexpress
TranscriptomicsBulk RNA-seq of the human fetal neocortex, lateral ganglionic eminence and medial ganglionic eminence at 7, 9, 11 and 20 post-conceptional weeks
Deep transcriptional profiling of the human neocortex, lateral ganglionic eminence (LGE) and medial ganglionic eminences (MGE), from 7 to 20 post-conceptional weeks (pcw), for de novo lincRNAs discovery and to establish a unique coding and non-coding gene signature for the three different regions.
ORGANISM(S): Homo sapiens 
2021-05-13 | E-MTAB-8893 | biostudies-arrayexpress
GenomicsSporadic autism exomes reveal a highly interconnected protein network of de novo mutations

It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no ...

phs000482.v1.p1 | EGA
GenomicsMolecular mechanism of action of plant DRM de novo DNA methyltransferases
DNA methylation is a conserved epigenetic gene regulation mechanism. DOMAINS REARRANGED METHYLTRANSFERASE (DRM) is a key de novo methyltransferase in plants, but how DRM acts mechanistically is poorly understood. Here, we report the crystal structure of the methyltransferase domain of tobacco DRM (N...
ORGANISM(S): Arabidopsis thaliana 
2014-05-27 | E-GEOD-54944 | biostudies-arrayexpress
TranscriptomicsDe Novo Assembly and Characterization of Stress Transcriptome in a salinity-Tolerant Variety CS52 of Brassica juncea
Oilseed mustard, Brassica juncea, exhibits high levels of genetic variability for salinity tolerance. To obtain the global view of transcriptome and investigate the molecular basis of salinity tolerance in a salt-tolerant variety CS52 of B. juncea, we performed transcriptome sequencing of control an...
ORGANISM(S): Brassica juncea 
2015-02-28 | E-GEOD-66389 | biostudies-arrayexpress
TranscriptomicsA Whole Transcriptional Linkage Analysis of Gene Co-Regulation in Insecticide Resistant House Flies, Musca domestica
Illumina HiSeq 2000 RNASeq was conducted on the mRNA fraction of three adult female Musca domestica strains. Two strains were the insecticide susceptible strains CS and aabys, which has five distinct recessive morphological markers, one on each of the five autosomes in M. domestica. The third strain...
ORGANISM(S): Musca domestica 
2014-01-02 | E-GEOD-39327 | biostudies-arrayexpress
TranscriptomicsOncogenic BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration [HT-seq]
Most cancer genomics papers to date have focused on aberrations in genomic DNA and protein-coding transcripts. However, around 50% of transcripts have no coding potential and may exist as non-coding RNA. We performed RNA-seq in BRAFv600e melanoma skin cancer and on melanocytes over-expressing oncoge...
ORGANISM(S): Homo sapiens 
2012-04-28 | E-GEOD-33092 | biostudies-arrayexpress
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