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| Status |
Public on Jun 19, 2019 |
| Title |
Root_CK_H3K9ac |
| Sample type |
SRA |
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| Source name |
shoot
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| Organism |
Oryza sativa |
| Characteristics |
age: two weeks
cultivar: Nipponbare
chip antibody: H3K9ac
tissue: shoot
treatment: control
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| Treatment protocol |
Leaves and root of two-week old rice cultivar ‘Nipponbare’ seedlings grown in green house were collected and ground into fine powder in liquid nitrogen. The resulting powder was suspended in nuclear isolation buffer (NIB: 20mM Tris-HCl, 50mM EDTA, 5mM Spermidine, 0.15mM Spermine, 0.1% mercaptoethanol, 40% Glycerol, pH 7.5) and followed the standard protocol for nuclei isolation.
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| Growth protocol |
Rice cultivar ‘Nipponbare’ seedlings grown in green house for two weeks
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Six commercial ChIP-grade antibodies, H3K9ac (Millipore, 07-352), H3K27ac (Abcam, ab4729), H3K27me3 (Millipore, 07-449), H3K36me3 (Abcam, ab9050), H4K12ac (Millipore, 07-595) and H3K4me3 (Abcam, ab8580), were used for ChIP experiments with leaf and root tissues,
ChIP libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The reads from ChIP-seq were aligned to rice genome (TIGR release 7) with one mismatch allowed using bowtie2 program. Only the reads mapped to a unique position of rice genome were included in the analysis.
macs14(version 1.4.2) is the software for peak calling, parameter -s SAM, -t, -c,--wig, --single, -g 3.8e+8 --bw 200 were used
Genome_build: rice (release 7)
Supplementary_files_format_and_content: wig files were generated using macs14,variableStep format andfixedStep format are included
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| Submission date |
Jan 25, 2018 |
| Last update date |
Jun 19, 2019 |
| Contact name |
Zheng dong yang |
| Organization name |
NJAU
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| Department |
college of agronomy
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| Lab |
wenlizhang
|
| Street address |
weigang NO.1
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| City |
Nanjing |
| ZIP/Postal code |
210000 |
| Country |
China |
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| Platform ID |
GPL13160 |
| Series (2) |
| GSE109616 |
Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice [ChIP-Seq] |
| GSE109618 |
Salt-responsive genes are differentially regulated at the chromatin level between the leaf and root tissues in rice |
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| Relations |
| BioSample |
SAMN08394929 |
| SRA |
SRX3599193 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2947280_H3K9ac_rootck_treat_afterfiting_all.wig.gz |
79.3 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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