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| Status |
Public on Mar 08, 2021 |
| Title |
RDM15_FLAG_Input_rep2 |
| Sample type |
SRA |
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| Source name |
seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Col0
genotype: RDM15
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| Growth protocol |
Plants were grown in air-conditioned rooms at 22 °C with 16 h-8 h light-dark cycle.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Preparation of DNA libraries for ChIP-Seq using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.
Genomic DNA was extracted from two-week-old seedlings using the Plant DNeasy mini kit (Qiagen).Total RNA extracted from two-week-old Col-0, rdm15-2 and rdm15-3 seedlings using the TRIzol (invitrogen) method.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Bisulfite-Seq: the raw data were trimmed using Trimmomatic (Bolger, Lohse, and Usadel 2014) with parameters "LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:50". Only clean paired-end reads were mapped to TAIR10 genome using tool BSMAP (Xi and Li 2009) with parameters "-m 0 -w 2" (other parameters were used the default value). To remove potential PCR duplicates, the "rmdup" command of SAMtools (Li et al. 2009) was used. methratio.py script from BSMAP was used to extract methylation ratios from mapping results.
Small RNA Sequencing: the adapter was removed using "fastx_clipper" command from FASTX-toolkit (http://hannonlab.cshl.edu/fastx_toolkit/index.html). After adapter sequences were trimmed, clean reads with size ranging from 18 to 31-nt were mapped to the Arabidopsis genome (TAIR10) using Bowtie (Langmead et al. 2009) with parameters "-v 0 -k 10". Reads that have overlap with annotated tRNAs, rRNAs, snRNAs, or snoRNAs were excluded.
ChIP-Seq: The paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana (TAIR10) with bowtie2 (Langmead and Salzberg 2012) with parameter "--very-sensitive --no-unal --no-mixed --no-discordant -k 5" . To remove potential PCR duplicates, markdup from SAMtools (Li et al. 2009) was used. After mapping, only uniquely mapped reads were retained.
Genome_build: TAIR10
Supplementary_files_format_and_content: Small RNA Sequencing: The bedGraph files for 24nt siRNAs were generated using genomeCoverageBed from bedtools with parameters "-bga -split".
Supplementary_files_format_and_content: For ChIP-Seq: The bedGraph files were generated using genomeCoverageBed from bedtools with parameters "-bg -pc".
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| Submission date |
Jul 13, 2020 |
| Last update date |
Mar 09, 2021 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
[email protected]
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| Organization name |
Purdue University
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| Department |
Department of Horticulture and Landscape Architecture
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| Street address |
625 Agriculture Mall Dr.
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| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
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| Platform ID |
GPL17639 |
| Series (1) |
| GSE154302 |
A histone H3K4me1 specific binding protein is involved in RdDM |
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| Relations |
| BioSample |
SAMN15517251 |
| SRA |
SRX8718707 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4668647_RDM15_FLAG_Input_rep2_unique_reads.bedGraph.gz |
80.1 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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