GSM2323948: OC 10M cage_seq; Macaca mulatta; RNA-Seq - SRA

SRX2182947: GSM2323948: OC 10M cage_seq; Macaca mulatta; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 11.8M spots, 3.6G bases, 1.4Gb downloads

Submitted by: NCBI (GEO)

Study: Spatiotemporal- and sex-specific Dynamics of lncRNA expression links to brain development and aging in Rhesus Macaque (CAGE-seq)

PRJNA343788 • SRP090245 • All experiments • All runs

show Abstracthide Abstract

Dynamic remodeling in architecture and function of mammalian brain, especially in primate, rely on a precisely orchestrated molecular and cellular regulation at distinct levels. Here, we applied comprehensive RNA-seq and CAGE-Seq analysis to characterize dynamics of lncRNA expression in Rhesus macaque brain across postnatal development and aging. We identified 18 anatomically diverse lncRNA modules and 14 mRNA modules representing spatial, age and sex specificities respectively. Highly spatiotemporal- and sex-specific dynamic changes in lncRNA but mRNA expression and the negative correlation between lncRNAs and mRNAs, functionally associate with brain development and aging, especially in the neocortex. Together with in situ hybridization (ISH) and quantitative real time-PCR (qRT-PCR) data, our findings provide an initial insight into spatial-, age- and sex-related dynamics of lncRNA expression during postnatal brain development and aging in macaque, implying that high dynamics of lncRNA expression might represent a previously unappreciated regulatory system in shaping brain architecture and function. Overall design: Examination of 8 different brain regions in Rhsesu Macaque across the four ages (1-, 4-, 10- and 20-year old )

Sample: OC 10M cage_seq

SAMN05799222 • SRS1706879 • All experiments • All runs

Organism: Macaca mulatta

Library:

Instrument: NextSeq 500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: CAGE

Layout: PAIRED

Construction protocol: For RNA-Seq library, total RNA was extracted from all the brain tissue samples by using TRIzol Reagent(Ambion) following the manufacturer’s instructions. Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). Total RNA was treated with RQ1 DNase (promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260 nm/280 nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% Agrose gel electrophoresis. For each sample, 10μg of total RNA was used for CAGE-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo(dT)-conjugated magnetic beads (invitrogen) .In brief, mRNA was treated with T4 polynucleotide kinase (NEB) at 37℃ for 30min and purified with oligo(dT)-conjugated magnetic beads (invitrogen). and subsequently degested with Terminator™ 5´-Phosphate-Dependent Exonuclease (Ambion) at 30℃ for 30min and purified with oligo(dT)-conjugated magnetic beads (invitrogen). The capped mRNA was performed with RT primer， then synthesized DNA with Terminal-Tagging oligo. The cDNAs were purified and amplified with PCR primers (illumina) and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 ℃ until used for sequencing.

Experiment attributes:

GEO Accession: GSM2323948

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 11.8M spots, 3.6G bases, 1.4Gb

Run	# of Spots	# of Bases	Size	Published
SRR4281308	11,775,248	3.6G	1.4Gb	2017-07-07

ID:: 3178163

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