|
| Status |
Public on Mar 08, 2021 |
| Title |
RDM15_FLAG_ChIP_rep1 (additional sequencing of GSM4668646) |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
chip antibody: FLAG
|
| Growth protocol |
Plants were grown in air-conditioned rooms at 22 °C with 16 h-8 h light-dark cycle.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was extracted from two-week-old seedlings using the Plant DNeasy mini kit (Qiagen).
Preparation of DNA libraries for ChIP-Seq using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina®.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
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: The bedGraph files were generated using genomeCoverageBed from bedtools with parameters "-bg -pc".
|
| |
|
| Submission date |
Aug 05, 2020 |
| Last update date |
Mar 09, 2021 |
| Contact name |
Jian-Kang Zhu |
| E-mail(s) |
zhu132@purdue.edu
|
| Organization name |
Purdue University
|
| Department |
Department of Horticulture and Landscape Architecture
|
| Street address |
625 Agriculture Mall Dr.
|
| City |
West Lafayette |
| State/province |
IN |
| ZIP/Postal code |
47907 |
| Country |
USA |
| |
|
| Platform ID |
GPL17639 |
| Series (1) |
| GSE154302 |
A histone H3K4me1 specific binding protein is involved in RdDM |
|
| Relations |
| BioSample |
SAMN15740711 |
| SRA |
SRX8894837 |
