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| Status |
Public on Jul 15, 2024 |
| Title |
YB2-FLAG, input |
| Sample type |
SRA |
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| Source name |
leaves
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaves
chip antibody: none
genotype: YB2-native-FLAG
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| Growth protocol |
The stratified seeds were germinated in half-strength Murashige and Skoog (MS) medium for 7 d and transferred to soil. Plants were grown under cool white light in a long-day condition (16 h light /8 h dark, 22 ºC).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, about 0.5-g 10-d-old seedlings were crosslinked with 1% formaldehyde and stopped with 125 mM glycine. Samples were ground and resuspended in the nuclei isolating buffer (10 mM Tris pH 8.0, 10 mM Sodium butyrate, 400 mM Sucrose, 0.1 mM PMSF, 5 mM β-mercaptoethanol, 1×cocktail protein inhibitor freshly). The isolated nuclei were resuspended with 1 mL lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM Sodium butyrate, 0.1% deoxycholate, 0.1% SDS, 1% Triton X-100, 1 mM PMSF and 1×protease inhibitor cocktail freshly) and sonicated into 200-500 bp fragments by Diagenode Bioruptor (high setting, 18 cycles，30s on and 30s off). Subsequently, the sonicated chromatin was incubated with anti-Flag M2 magnetic beads (Sigma, M8823) overnight at 4°C.
The recovered DNAs in ChIP assay were used to library construction with the Scale ssDNA-seq Lib Prep Kit (ABclonal, RK20228). High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
The clean paired-end reads were mapped to the reference genome by Bowtie2 (Version 2.3.5) and reads with low mapping quality or multiple positions on the genome were identified and removed by SAMtools (version 1.9). Only perfectly and uniquely mapped reads were retained for further analysis.
Enriched peaks were called and annotated by MACS2 (Version 2.2.8) with the following parameters: “-f BAMPE -g 119145879 -q 0.01”. Peaks that were consistently found in two replicates were selected for further analyses. The generated data were imported into the Integrative Genomics Viewer (IGV) (James T Robinson, 2011) for visualization.
ComputeMatrix, plotProfile and plotHeatmap programs in deepTools (version 3.3.0) were used to compare the average enrichment at defined loci between YB2-FLAG and WT. To assign peaks to proximal genes, regions within 1.0 kb flanking the transcription start site (TSS) were extracted.
Assembly: TAIR10
Supplementary files format and content: bedGraph files generated from SAMtools
Supplementary files format and content: peak files generated from MACS2
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| Submission date |
Nov 06, 2023 |
| Last update date |
Jul 15, 2024 |
| Contact name |
Chuyu Lin |
| E-mail(s) |
12316066@zju.edu.cn
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| Phone |
+86 13588301175
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| Organization name |
Zhejiang University
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| Department |
College of Agriculture and Biotechnology
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| Lab |
Tao’s Lab
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| Street address |
866#, Yuhangtang Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL26208 |
| Series (2) |
| GSE247053 |
A pair of NUCLEAR FACTOR Y transcription factors act as positive regulators in jasmonate signaling and disease resistance in Arabidopsis |
| GSE247055 |
A pair of NUCLEAR FACTOR Y transcription factors act as positive regulators in jasmonate signaling and disease resistance in Arabidopsis |
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| Relations |
| BioSample |
SAMN38114620 |
| SRA |
SRX22378893 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7882699_input.bedGraph.gz |
146.7 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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