|
| Status |
Public on Feb 25, 2017 |
| Title |
nrpe1 ΔSD rep1 |
| Sample type |
SRA |
| |
|
| Source name |
nrpe1 ΔSD mutant
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col-0
background: nrpe1-11 mutant
nrpe1 construct: NRPE1ΔSD
tissue: 2.5 week above ground tissues
|
| Treatment protocol |
Transgenic lines were selected for by spraying with Basta herbicide
|
| Growth protocol |
Plants were grown in soil in long day conditions (16h light, 8 hours dark)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
CTAB extraction of genomic DNA from 2.5 week above ground tissues
Illumina TruSeq DNA methylation Kit (product number: EGMK81312)
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Index 1
|
| Data processing |
Base-calling, adapter trimming, and size selection (>35bp) was completed with bcl2fastq v2.16.0.10
Methylation end bias was removed and reads were quality filtered using cutadapt v. 1.9.1 with the commands: cutadapt -U 7 -u 2 -q 25
Filtered reads were mapped to the TAIR10 genome and mapped reads were deduplicated using Bismark 0.16.1 using default settings.
Methylation status of each cytosine was extracted from mapped reads using Bismark_methylation_extractor with the commands: bismark_methylation_extractor -p --bedGraph --CX -cutoff 5 --cytosine_report --CX
Methylation status of each cytosine in the CHH context was extracted from the bismark_methylation_extractor output and used as input to the R package, methylkit v. 0.9.5 to define differentially methylated regions (DMRs) relative to Col-0. The genome was split into 300 base pair sliding windows with a step size of 200 base pairs and a minimum coverage requirement for each window of 10 informative cytosines with at least 5 read coverage each. Only regions that had coverage in each sample were utilized for calculation of DMRs. Significant hypo-DMRs were defined as those regions with a minimum 25% decrease in methylation relative to Col-0 and a q-value of less than or equal to 0.01.
Genome_build: TAIR10
Supplementary_files_format_and_content: Tab delimited text files that include methylation status of cytosines in the CHH context with at least 5 read coverage. Format for input to R package methylkit
|
| |
|
| Submission date |
Jan 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jered Wendte |
| Organization name |
Indiana University
|
| Street address |
915 E. 3rd Street
|
| City |
Bloomington |
| State/province |
IN |
| ZIP/Postal code |
47405 |
| Country |
USA |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE93358 |
Functional analysis of the Arabidopsis thaliana Pol V largest subunit, NRPE1, carboxy-terminal domain by whole genome bisulfite sequencing |
| GSE93360 |
Functional analysis of the RNA polymerase V CTD |
|
| Relations |
| BioSample |
SAMN06214620 |
| SRA |
SRX2481041 |
