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| Status |
Public on Aug 22, 2020 |
| Title |
Maize_B73_ATAC_root_rep2 |
| Sample type |
SRA |
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| Source name |
B73 Root
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| Organism |
Zea mays |
| Characteristics |
cultivar: B73
tissue: root
age: 6 days
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| Treatment protocol |
No Treatment
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| Growth protocol |
For maize root ATAC-seq data generated in this study, Z. mays (accession B73) were grown in soil for around 6 days at 25 °C under 16 h light–8 h dark. The staple roots were harvested and were used for experiments.
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| Extracted molecule |
genomic DNA |
| Extraction 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.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
Rep 2 B73 Root ATAC_seq
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| Data processing |
ATAC-seq raw reads were aligned as described before (Lu, et al. 2019; Ricci, et al. 2019). Raw reads were trimmed with Trimmomatic v.0.33. Reads were trimmed for NexteraPE with a maximum of two seed mismatches, a palindrome clip threshold of 30 and a simple clip threshold of ten. Reads shorter than 30 bp were discarded. Trimmed reads were aligned to the Z. mays AGPv4 reference genome using Bowtie v.1.1.1 with the following parameters: ‘bowtie -X 1000 -m 1 -v 2 --best –strata’. Aligned reads were sorted using SAMtools v.1.3.1 and clonal duplicates were removed using Picard version v.2.16.0 (http://broadinstitute.github.io/picard/). MACS2 was used to define ACRs with the ‘-keepdup all’ function and with ATAC-seq input samples (Tn5 transposition into naked gDNA) as a control.
The ACRs identified by MACS2 were further filtered using the following steps: (1) peaks were split into 50 bp windows with 25 bp steps; (2) the accessibility of each window was quantified by calculating and normalizing the Tn5 integration frequency in each window with the average integration frequency across the whole genome to generate an enrichment fold value; (3) windows with enrichment fold values passing a cutoff (30-fold) were merged together by allowing 150 bp gaps and (4) possible false positive regions were removed by filtering small regions with only one window for lengths >50 bp. The sites within ACRs with the highest Tn5 integration frequencies were defined as ACR ‘summits’.
Genome_build: Z. mays genome and gene annotation AGPv4
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| Submission date |
Jun 08, 2020 |
| Last update date |
Aug 22, 2020 |
| Contact name |
Robert J Schmitz |
| E-mail(s) |
schmitz@uga.edu
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| Organization name |
University of Georgia
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| Department |
Genetics
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| Street address |
B416 Davison Life Sciences
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| City |
Athens |
| State/province |
GA |
| ZIP/Postal code |
30602 |
| Country |
USA |
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| Platform ID |
GPL20156 |
| Series (1) |
| GSE152046 |
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes |
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| Relations |
| BioSample |
SAMN15172222 |
| SRA |
SRX8499541 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4600941_B73Root2.bed.gz |
287.0 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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