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SRX13439212: GSM5736278: 12-M-1; Mus musculus; OTHER
1 ILLUMINA (Illumina NovaSeq 6000) run: 5M spots, 1.5G bases, 562.6Mb downloads

Submitted by: NCBI (GEO)
Study: Complex Genomic Patterns of Abasic Sites in Mammalian DNA Revealed by High-Resolution SSiNGLe-AP Method
show Abstracthide Abstract
DNA damage plays critical role in biology and disease, however, precise understanding of how different types of DNA damage affect cellular functions is far from clear. A major underlying reason for this is paucity of high-resolution methods that can map locations of different types of DNA damage in complex genomes such as those of mammals. Here, we present development and validation of SSiNGLe-AP method that can map a common type of DNA damage, abasic (AP) sites, genome-wide and with high-resolution. We applied this method to six different tissues of mice of different ages and human cancer cell lines. We found non-random distribution of AP sites in mammalian genome that exhibits dynamic enrichment at specific genomic locations, and is significantly influenced by gene expression, age and especially by tissue-type. Overall, these results suggest that we are at the very beginning of understanding the true complexities of genomic patterns of DNA damage. Overall design: Development of high-resolution SSiNGLe-AP method to map AP sites genome-wide and its application to reveal genomic patterns of AP sites in different mouse tissues of different ages
Sample: 12-M-1
SAMN24060776 • SRS11338632 • All experiments • All runs
Organism: Mus musculus
Library:
Instrument: Illumina NovaSeq 6000
Strategy: OTHER
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: 12 male mice of C57BL/6J strain from 4 age groups (3-, 12-, 19- and 22-month-old) were used to extract brains, hearts, livers, bone marrow, PBMCs and sperms. Red cells in bone marrow were removed by Red Blood Cell Lysis Buffer (Beyotime). PBMCs were isolated from blood using Ficoll-Paque PLUS (GE Healthcare). The motile spermatozoa were isolated from the mouse epididymal tail by collecting cells floating in the upper layer of RPMI 1640 (Thermo Fisher Scientific). The isolated tissues were immediately put into liquid nitrogen for quick freezing. The whole organs were cut into small pieces and ground into powder by tissue homogenizer in presence of liquid nitrogen to avoid heating. All ground tissue samples were stored at -80℃ prior to DNA isolation. Genomic DNA from the mouse brain, bone marrow, heart, liver and PBMCs was isolated using TIANamp Genomic DNA kit (Tiangen, DP304) with RNaseA treatment according to the manufacturer's protocols. Genomic DNA from sperm cells was extracted using Sperm DNA Purification Kit (Simgen, 4202050) following the manufacturer's instructions. All DNA samples were eluted in UltraPure™ DNase/RNase-Free Distilled Water (Invitrogen), measured the concentration using SMA6000 (Merinton) and stored at -20℃. SSiNGLe-AP method
Experiment attributes:
GEO Accession: GSM5736278
Links:
Runs: 1 run, 5M spots, 1.5G bases, 562.6Mb
Run# of Spots# of BasesSizePublished
SRR172609285,014,3121.5G562.6Mb2022-11-10

ID:
18595249

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