GSM1960360: Naked Mole Rat Adult Liver 3; Heterocephalus glaber; RNA-... - SRA

SRX1458827: GSM1960360: Naked Mole Rat Adult Liver 3; Heterocephalus glaber; RNA-Seq
1 ILLUMINA (Illumina HiSeq 2500) run: 35.5M spots, 7.2G bases, 4.3Gb downloads

Submitted by: NCBI (GEO)

Study: DNA repair in species with extreme lifespan differences

PRJNA304727 • SRP066912 • All experiments • All runs

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We compared RNA-seq expression patterns in liver, an organ with high oxidative metabolism and abundant spontaneous DNA damage, from humans, naked mole rats, and mice, differing in maximum lifespan over a range of ~100, 30, and 3 years, respectively, for 130 genes involved in DNA repair. The results show that the longer-lived species, human and naked mole rat, share higher expression of these DNA repair genes, including core genes in several DNA repair pathways. A more systematic approach of signaling pathway analysis (SPA) indicates statistically significant upregulation of several DNA repair signaling pathways in human and naked mole rat compared with mouse. Overall design: Compare steady-state RNA levels from 3 samples each of adult liver tissue of human, naked mole rat, and mouse. Mouse samples available in the Short Reads Archive: SRX871336, SRX871370, SRX871395 (SRP053350) and BioProject PRJNA274780.

Sample: Naked Mole Rat Adult Liver 3

SAMN04308759 • SRS1186282 • All experiments • All runs

Organism: Heterocephalus glaber

Library:

Instrument: Illumina HiSeq 2500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: Harvested livers were preserved in RNAlater (ThermoFisher Scientific) Total RNA quality was checked on an Agilent 2100 Bioanalyzer; only samples with a RNA Integrity Number greater than 8.5 were used for subsequent analysis. Total RNA was treated with DNaseI, column purified using the miRNeasy Mini Kit (Qiagen), and depleted of ribosomal RNA with Ribo-Zero Magnetic Gold Kit (Epicentre), followed by ethanol precipitation. Depleted RNA was converted to cDNA using SuperScript III First-Strand Synthesis Kit (Invitrogen) with 80 ng random hexamers and 50 μM oligo dT and subsequently ethanol precipitated. Single-stranded cDNA was converted to dsDNA by DNA polymerase I while incorporating dU/VTPs (10 mM). Samples were fragmented in 1 × TE to 200–300 bp using Covaris. After fragmentation, samples were purified using the MinElute PCR purification kit (Qiagen). Fragmented samples underwent standard end-repair, dA-tailing and adapter ligation using Illumina TruSeq adapters for multiplexing. Adapter-ligated cDNA was treated with uracil-DNA glycosylase followed by enrichment PCR using Q5 polymerase (New England Biolabs) for 18 cycles. Libraries were size selected for 150–600 bp on a 2% low-melt ultra low-range agarose gel stained with SYBR Gold (Invitrogen) to eliminate adaptor dimers.

Experiment attributes:

GEO Accession: GSM1960360

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 35.5M spots, 7.2G bases, 4.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR2969600	35,540,245	7.2G	4.3Gb	2015-12-04

ID:: 2063493

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