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SRX8499541: GSM4600941: Maize_B73_ATAC_root_rep2; Zea mays; ATAC-seq
1 ILLUMINA (NextSeq 500) run: 101.3M spots, 7.3G bases, 2.7Gb downloads

Submitted by: NCBI (GEO)
Study: Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
show Abstracthide Abstract
The genomic sequences of diverse varieties of many crop species continue to be produced at a frenetic pace. However, it remains challenging to develop complete annotations of functional genes and regulatory elements in these genomes. Here, we explore the potential to use DNA methylation profiles to develop more complete and refined annotations. Using leaf tissue in maize, we define ~100,000 unmethylated regions (UMRs) that account for 5.8% of the genome; 33,375 UMRs (1.3% of the genome) are found greater than 2 kilobase pairs from genes. UMRs are highly stable in multiple vegetative tissues and they capture the vast majority of accessible chromatin regions from leaf tissue. However, many UMRs are not accessible in leaf (leaf-iUMRs) and these represent a set of genomic regions with potential to become accessible in specific cell types or developmental stages. Leaf-iUMRs often occur near genes that are expressed in other tissues and are enriched for transcription factor (TF) binding sites of TFs that are also not expressed in leaf tissue. The leaf-iUMRs exhibit unique chromatin modification patterns and are enriched for chromatin interactions with nearby genes. The total UMRs space in four additional monocots ranges from 80-120 megabases, which is remarkably similar considering the range in genome size of 271 megabases to 4.8 gigabases. In summary, based on the profile from a single tissue, DNA methylation signatures pinpoint both accessible regions and regions poised to become accessible or expressed in other tissues. Thus, UMRs can provide powerful filters to distill large genomes down to the small fraction putative functional elements and facilitate the discovery of tens of thousands of novel candidate regulatory regions. Overall design: ATAC–seq maize B73 root tissue, duplicate samples.
Sample: Maize_B73_ATAC_root_rep2
SAMN15172222 • SRS6798252 • All experiments • All runs
Organism: Zea mays
Library:
Instrument: NextSeq 500
Strategy: ATAC-seq
Source: GENOMIC
Selection: other
Layout: PAIRED
Construction protocol: ATAC-seq was performed as described previously (Lu et al 2017). For each replicate, approximately 100 mg of maize staple roots were harvested and immediately chopped with a razor blade and placed in 2 ml of pre-chilled lysis buffer (15 mM Tris–HCl pH 7.5, 20 mM sodium chloride, 80 mM potassium chloride, 0.5 mM spermine, 5 mM 2-mercaptoethanol and 0.2% TritonX-100). The chopped slurry was filtered twice through miracloth. The crude nuclei were stained with 4,6-diamidino- 2-phenylindole and loaded into a flow cytometer (Beckman Coulter MoFlo XDP). Nuclei were purified by flow sorting and washed in accordance with (Lu et al 2017). The sorted nuclei (50,000 nuclei per reaction) were incubated with 2 μl of transposome in 40 μl of tagmentation buffer (10 mM TAPS–sodium hydroxide pH 8.0, 5 mM magnesium chloride) at 37 °C for 30 min without rotation. The integration products were purified using a NEB Monarch PCR Purification Kit and then amplified using Phusion DNA polymerase for 11 cycles (Buenrostro et al 2013). Amplified libraries were purified with AMPure beads to remove primers.
Experiment attributes:
GEO Accession: GSM4600941
Links:
Runs: 1 run, 101.3M spots, 7.3G bases, 2.7Gb
Run# of Spots# of BasesSizePublished
SRR11955291101,287,2997.3G2.7Gb2020-08-24

ID:
11051577

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