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| Status |
Public on Jun 10, 2022 |
| Title |
SYN4-ChIP-biological replicate 2 |
| Sample type |
SRA |
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| Source name |
the 7-day-old whole seedlings
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| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: the 7-day-old whole seedlings
genotype: Col-0
chip antibody: anti-GFP (Abcam #ab290)
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| Growth protocol |
Plants were grown at 21℃ on MS agar plates supplemented with 1.5% sucrose and 0.8% agar.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Briefly, 10 g fresh 7-day-old whole seedlings were cross-linked in the cross-link buffer (0.4 M sucrose, 10m M Tris-HCl (pH8.0), 1m M PMSF, 1 m M EDTA, 1% formaldehyde) for 3×5min using vacuum infiltration and the reaction was terminated in 2 M glycine.
After reverse cross-link, DNA was extracted by phenol-chloroform method and sheared to an average size of 300 bp using a sonicator.Sequencing library was constructed according to the standard Illumina protocol.First,the end was supplemented, adenine was added in the 3 'segment, and then PCR amplification technology was used to build the library.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 1500 |
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| Data processing |
Low-quality and adapter sequences were trimmed from the reads using cutadapt (v1.18) with parameters: -a AGATCGGAAGAGC -A AGATCGGAAGAGC --trim-n -m 50 -q 20, 20.
Then, the reads were mapped to the Arabidopsis thaliana TAIR10 genome using Bowtie2 (v2.3.4.3) with parameters: -N 0 --no-discordant --no-mixed --no-unal.
Samtools (v1.9) was used to transfer the mapping results from sam format to position sorted bam format.
Next, the duplicated reads were removed by markdup from sambamba (v0.6.8).
Bam files were then converted to bigwig files using bamCoverage from the deeptools suite (v3.1.3) with parameters: --normalize using RPKM --binSize 25.
Assembly: TAIR10
Supplementary files format and content: bigWig(bigWig is the binary version of WIG or bedGraph. BigWig stores interval axis information. And correlation score (SCORE), mainly used to view continuous density maps of data in the Genome Browser)
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| Submission date |
Jun 08, 2022 |
| Last update date |
Jun 10, 2022 |
| Contact name |
Yu Zhang |
| E-mail(s) |
[email protected]
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| Organization name |
Shanghai Jiaotong University
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| Street address |
DongChuan Road No. 800
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| City |
shanghai |
| ZIP/Postal code |
200030 |
| Country |
China |
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| Platform ID |
GPL19080 |
| Series (1) |
| GSE205736 |
H2A monoubiquitination targeting by cohesin subunits in Arabidopsis |
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| Relations |
| BioSample |
SAMN16930342 |
| SRA |
SRX9596260 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6222428_SYN4_2.bw |
25.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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