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| Status |
Public on Jun 21, 2020 |
| Title |
brm-1_BRIP1-GFP-IP-bio2 |
| Sample type |
SRA |
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| Source name |
Young seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Seedling
developmental stage: 14-day-old
antibody: none
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| Growth protocol |
Plants were grown in 1/2MS media with 22 degree in 16h light/8h dark
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated protein-DNA complexes were isolated with GFP antibody.
Two ng of ChIP DNA immuoprecipitated by anti-GFP antibody was used for ChIP-seq library construction. Blunting end, adapter ligation and amplification were carried out using Illumina Genomic DNA Sample Prep Kits according to the manufacturer's protocol. Illumina Novaseq was used for high-throughput sequencing of the ChIP-seq library.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
brm-1_BRIP1-GFP-IP-bio2
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| Data processing |
The raw reads were mapped to the reference genome (Arabidopsis thaliana genome, TAIR10) with Bowtie for Illumina (Galaxy Version 1.1.2) for DNA sequencing on web https://usegalaxy.org/ with default setting, except that the paired-end was required.
MACS2 (Galaxy Version 2.1.1) was used for peak calling using the following parameters “gsize=119,667,750, bw=300, q=0.01, nomodel, extsize=200”.
The alignments were first converted to Wiggle (WIG) files and the bigwig files were generated using bamCoverage with “-bs 10”, “--normalizeUsing RPKM (reads per kilobase per million)” in DeepTools and then the data were imported into the Integrative Genomics Viewer (IGV) for visualization.
Genome_build: TAIR10
Supplementary_files_format_and_content: peaks.narrowPeak
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| Submission date |
Apr 21, 2020 |
| Last update date |
Jun 22, 2020 |
| Contact name |
yaoguang yu |
| Organization name |
SUN YAT-SEN UNIVERSITY
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| Street address |
No. 135, Xingang Xi Road
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| City |
Guangzhou |
| ZIP/Postal code |
510275 |
| Country |
China |
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| Platform ID |
GPL26208 |
| Series (1) |
| GSE142621 |
Genome-wide profiling of SWI/SNF chromatin remodeler BRAHMA (BRM) and BRM Interacting Protein 1/2 (BRIP1/2) in Arabidopsis |
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| Relations |
| BioSample |
SAMN14651802 |
| SRA |
SRX8148226 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4487487_brm-1_BRIP1-GFP-IP-bio2_peaks.narrowPeak.gz |
101.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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