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Sample GSM2704260 Query DataSets for GSM2704260
Status Public on Jul 26, 2017
Title Mt_root.tip.ATAC_rep2
Sample type SRA
 
Source name Root tip
Organism Medicago truncatula
Characteristics strain/background: A17
tissue or cell type: 1 cm root tip
nuclei purification method: INTACT streptavidin affinity purification
Treatment protocol One centimeter root tips or fully differentiated root zone (above first fully expanded root hairs but below any lateral roots) were harvested using a razor blade. Total root tip nuclei were purified using INTACT affinity purification or by tissue lysis followed by sucrose sedimentation. Arabidopsis root hair and non-hair cell nuclei were purified by INTACT from the fully differentiated root zones.
Growth protocol All plants were grown under 16hr light/8 hr dark cycles on vertically-oriented nutrient agar plates.
Extracted molecule genomic DNA
Extraction protocol Tn5 Transposase treatment (using the Illumina Nextera kit) was performed on 50,000 nuclei from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit.
Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers, followed by purification of library fragments using SPRI beads.
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description Mtc2
Data processing Raw reads were aligned to the appropriate genome using Bowtie2 with default parameters.
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks (transposase hypersensitive sites; THSs) were identified using the Findpeaks function of the Homer package, with the parameters "-region" and "-minDist 150". Bed files of the THS regions are included for each dataset.
Genome_build: Arabidopsis thaliana TAIR10, Medicago truncatula Mt4.0, Solanum lycopersicum SL2.4, and Oryza sativa IRGSP 1.0.30
Supplementary_files_format_and_content: .bed files containing ATAC-seq transposase hypersensitive site locations as defined using the findPeaks function of the Homer software package.
 
Submission date Jul 14, 2017
Last update date May 15, 2019
Contact name Roger B Deal
E-mail(s) roger.deal@emory.edu
Phone 404-727-8087
Organization name Emory University
Department Biology
Street address 1510 Clifton Rd NE
City Atlanta
State/province GA
ZIP/Postal code 30322
Country USA
 
Platform ID GPL21643
Series (1)
GSE101482 ATAC-seq profiling of open chromatin in the root tips of four plant species (Arabidopsis thaliana, Medicago truncatula, Solanum lycopersicum, and Oryza sativa) and two Arabidopsis thaliana cell types (root hair and non-hair epidermal cells)
Relations
BioSample SAMN07352896
SRA SRX3006639

Supplementary file Size Download File type/resource
GSM2704260_Mt_root.tip.ATAC_rep2_homer.region.mD150.bed.gz 314.8 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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