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Sample GSM1399653 Query DataSets for GSM1399653
Status Public on Jun 06, 2014
Title gSELEXx9
Sample type SRA
 
Source name mature leaves from 3 week old plants
Organism Arabidopsis thaliana
Characteristics ecotype: WT, columbia
tissue: mature leaves
age: 3 weeks
Growth protocol All plants were grown under long day conditions.
Extracted molecule genomic DNA
Extraction protocol For the genomic SELEX experiment, Arabidopsis thaliana genomic DNA was extracted from wild type 3 week old plant leaves and fragmented to 100 bp using COVARIS. 2 μg of this DNA was processed for end repair and adaptor ligation following the manufacturer’s instructions (Illumina) and used as indicated above for incubation with purified GST-SUVR5 zinc finger domain protein. Two genomic SELEX experiments were performed, one using only one binding/eluting cycle (x1: control) and one with 9 cycles (x9). The recovered DNA was sequenced using an Illumina Genome Analyzer.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina Genome Analyzer
 
Data processing Library strategy: SELEX
Reads were mapped to the genome using Bowtie (Langmead et al., Genome Biol 2009) allowing up to two mismatches and only retaining uniquely mapping reads.
gSELEX peaks were defined using MACS (Zhang et al., Genome Biol 2008) with the following parameters: band width = 100, model fold =32, p<1e-10, and for the definition of SELEX peaks we considered a peak positive when it showed over 50 fold increase.
Genome_build: TAIR8
Supplementary_files_format_and_content: Column 1: chromosome, Column 2: start, Column3: stop
 
Submission date May 28, 2014
Last update date May 15, 2019
Contact name Hume Stroud
Organization name UT Southwestern
Street address 5323 Harry Hines Blvd
City Dallas
State/province TX
ZIP/Postal code 75390
Country USA
 
Platform ID GPL9062
Series (2)
GSE39405 The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner
GSE58034 The SET-domain protein SUVR5 mediates H3K9me2 deposition and silencing at stimulus response genes in a DNA methylation independent manner [SELEX]
Relations
BioSample SAMN02840821
SRA SRX574355

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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