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| Status |
Public on Apr 10, 2021 |
| Title |
FVE_ChIPSeq_Rep1 |
| Sample type |
SRA |
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| Source name |
Seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
antibody: FLAG
background: fve-4 backgroud
tissue: seedlings
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| Growth protocol |
Plants were grown at 22°C in a growth chamber with 16 h of light and 8 h of darkness on 1/2 MS medium with 0.8% glucose.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP samples were sent to the Genomics Core Facilities of the Shanghai Center for Plant Stress Biology, CAS (Shanghai, China) for library construction and Illumina sequencing.
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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 |
Adapter and 3’-end of reads with sufficiently low quality scores (q<20) were trimmed, and clean reads that were shorter than 45 nt were discarded.
Clean paired-end reads were mapped to the TAIR10 genome of Arabidopsis thaliana with Bowtie2 (version 2.3.4.1) with default parameters (Langmead and Salzberg, 2012)
Samtools (Li et al., 2009) was used to remove potential PCR duplicates; only uniquely aligned reads were retained for the downstream analysis.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files that represent the number of reads at each position in genome normalized to the average base-pair count number
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| Submission date |
Apr 09, 2021 |
| Last update date |
Apr 11, 2021 |
| Contact name |
Pei Huang |
| Organization name |
Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences (CAS), Shanghai
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| Street address |
Fenglin Road 300
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| City |
Shanghai |
| ZIP/Postal code |
201602 |
| Country |
China |
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| Platform ID |
GPL17639 |
| Series (1) |
| GSE171808 |
FVE directly enriches to RdDM target loci. |
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| Relations |
| BioSample |
SAMN18686767 |
| SRA |
SRX10566680 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5234532_ATCS-285.cpm.bw |
39.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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