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Status |
Public on Jun 06, 2014 |
Title |
gSELEXx9 |
Sample type |
SRA |
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Source name |
mature leaves from 3 week old plants
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Organism |
Arabidopsis thaliana |
Characteristics |
ecotype: WT, columbia tissue: mature leaves age: 3 weeks
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Growth protocol |
All plants were grown under long day conditions.
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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.
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Library strategy |
OTHER |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina Genome Analyzer |
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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
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Submission date |
May 28, 2014 |
Last update date |
May 15, 2019 |
Contact name |
Hume Stroud |
Organization name |
UT Southwestern
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Street address |
5323 Harry Hines Blvd
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City |
Dallas |
State/province |
TX |
ZIP/Postal code |
75390 |
Country |
USA |
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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] |
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Relations |
BioSample |
SAMN02840821 |
SRA |
SRX574355 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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