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Sample GSM2260236 Query DataSets for GSM2260236
Status Public on Nov 30, 2016
Title Col-0_50k_root_nuclei_FANS-ATAC-seq_rep2
Sample type SRA
 
Source name Col-0_50k_root_nuclei_FANS-ATAC-seq
Organism Arabidopsis thaliana
Characteristics ecotype background: Col-0
genotype/variation: wild type
tissue: roots
age: 7days
Growth protocol The Arabidopsis thaliana accession Col-0 and 35S:H2AX-GFP transgenic plants were grown on a vertical plate with ½ LS media and 1% sugar in long day light conditions (16 hours light / 8 hours dark) for 7-8 days.
Extracted molecule genomic DNA
Extraction protocol Nuclei were isolated by chopping fresh whole seedlings or roots, density gradient centrifugation and then FANS. Tn5 integration were performed with 50,000 or as less as 500 purified nuclei. Libraries were constructed with 10-13 cycles amplafication of the Tn5 integration products.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing library strategy: FANS-ATAC-seq
maize_B73_overground_part_FANS-ATAC-seq_1million_reads were mapped to maize B73_5a and the others to the TAIR 10
Regulatory regions were called by HOTSPOT and footprints identified by pyDNase
Genome_build: TAIR 10
Supplementary_files_format_and_content: *BED file, the identified regulatory regions
Supplementary_files_format_and_content: *BW file, the genome coverage of each sample, BigWig format
 
Submission date Aug 04, 2016
Last update date May 15, 2019
Contact name Robert J Schmitz
E-mail(s) schmitz@uga.edu
Organization name University of Georgia
Department Genetics
Street address B416 Davison Life Sciences
City Athens
State/province GA
ZIP/Postal code 30602
Country USA
 
Platform ID GPL19580
Series (1)
GSE85203 Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes
Relations
BioSample SAMN05513132
SRA SRX2000804

Supplementary file Size Download File type/resource
GSM2260236_Col-0_50k_root_nuclei_FANS-ATAC-seq_rep2.bw.gz 68.9 Mb (ftp)(http) BW
GSM2260236_Col-0_50k_root_nuclei_FANS-ATAC-seq_rep2.regulatory_region.bed.gz 250.3 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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