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SRX3395587: GSM2857919: WT, rep2; Arabidopsis thaliana; RNA-Seq
1 ILLUMINA (NextSeq 550) run: 38.6M spots, 2.9G bases, 1.2Gb downloads

Submitted by: NCBI (GEO)
Study: Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds [RNA-seq]
show Abstracthide Abstract
We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. To further investigate the downstream targets of REF6 represented H3K27me3 demethylase, we performed RNA-seq using single, double mutant and triple mutant. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me3 demethylase, the binding targets of DNA binding domain deleted REF6 were identified in the triple mutant background in which REF6 and its two homologs were mutated. Meanwhile, the H3K27me3 marked regions in both wild type and triple mutant flowers were defined. By analyzing the differentially enriched H3K27me3 region and REF6 binding profile, we found that REF6 functions to determine the boundary of H3K27me3 regions. Comparison of binding profiles of REF6 in flowers and in seedlings (ref) revealed a tissue-specific binding manner. More importantly, we found that the indirect binding of REF6 is mediated by trans factors and this indirect binding is crucial for REF6 function, especially in reproductive organs in Arabidopsis. Our results provide novel molecular insights into REF6 functions. Overall design: Expression profiling by RNA-seq in different genetic backgrounds of Arabidopsis.
Sample: WT, rep2
SAMN08028669 • SRS2689770 • All experiments • All runs
Library:
Instrument: NextSeq 550
Strategy: RNA-Seq
Source: TRANSCRIPTOMIC
Selection: cDNA
Layout: SINGLE
Construction protocol: Total RNAs from 5-week-old flowers of wild-type, ref6-3, ref6C, elf6-3ref6C and elf6-3ref6Cjmj13G were isolated by using the RNeasy Plant Mini Kit (Qiagen, Germany) according to manufacturer. 2 μg total RNA was used to produce libraries using TruSeq Stranded Total RNA LT Sample Prep Kit (Illumina, USA). Pooled libraries were submitted to a NextSeq®550 sequencing platform (Illumina, USA) for sequencing.
Experiment attributes:
GEO Accession: GSM2857919
Links:
Runs: 1 run, 38.6M spots, 2.9G bases, 1.2Gb
Run# of Spots# of BasesSizePublished
SRR629448438,586,7862.9G1.2Gb2018-07-09

ID:
4735100

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