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| Status |
Public on Mar 10, 2012 |
| Title |
chd1 H3K27me3_ChIPSeq |
| Sample type |
SRA |
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| Source name |
chd1(chr729)
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| Organism |
Oryza sativa Japonica Group |
| Characteristics |
developmental stage: 11 days seedling
cell type: Full plants
chip antibody: H3K27me3
vendor: Millipore, DAM166204
genotype/variation: chd1(chr729)
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| Growth protocol |
The rice grew under long day conditions (14.5 h light and 8.5 h dark per day) and 28 C in the rooting medium.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Full plant of 11 days old rice seedlings which were grew under the conditions (14.5h light and 8.5h dark at 28C) in the rooting medium were used for chromatin immunoprecipitation (CHIP) experiments. During the experiments, Chromatin was fragmented to 100-500bp by sonication and ChIP was performed using the following two antibodies: H3K4me3 (Millipore, DAM1731494) and H3K27me3 (Millipore, DAM166204). Briefly, The precipitated DNA was end-repaired using a combination of T4 DNA polymerase (Catalog NO.P708L), and T4 polynucleotide kinase (Catalog NO.Y904L). The blunt, phosphorylated ends were treated with Klenow Enzyme(Catalog NO.P706L) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3â end, all of above as discribled according to Illumina Paired-End DNA Sample Prep kit. After adapter ligation DNA was PCR amplified with Illumina primers and library fragments of 100~300 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced with the Equipment Illumina HISEQ2000.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Chromatin IP against H3K27me3
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| Data processing |
Clean: After completing the sequencing,we removed the low-quality sequences, the adaptor sequences, and the pollutions.
Alignment: Sequence reads were obtained and mapped to the rice (Orazy JP_6.1) genomes using SOAP2.21 software. All reads mapping with two or fewer mismatches were retained and read starts were summed in sliding windows of 50 bp to create summary windows.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm, the default parameters were bandwidth, 200bp; mfold, 32; P-value of 1.00e-05.
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| Submission date |
Jul 07, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
yongfeng hu |
| E-mail(s) |
feng2602@sina.com
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| Organization name |
IBP
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| Street address |
univercite paris-sud Bat 630
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| City |
paris |
| ZIP/Postal code |
91400 |
| Country |
France |
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| Platform ID |
GPL13834 |
| Series (1) |
| GSE30490 |
Genome-wide maps of H3K4me3 and H3K27me3 in HY(Hwayong) and chd1(chr729) rice. |
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| Relations |
| SRA |
SRX082185 |
| BioSample |
SAMN00632348 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM756377_chd_K27me3.bed.200_peaks.txt.gz |
35.9 Kb |
(ftp)(http) |
TXT |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr01_13101.wig.gz |
2.1 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr02_13102.wig.gz |
1.8 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr03_13103.wig.gz |
1.8 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr04_13104.wig.gz |
1.6 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr05_13105.wig.gz |
1.4 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr06_13106.wig.gz |
1.5 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr07_13107.wig.gz |
1.4 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr08_13108.wig.gz |
1.2 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr09_13109.wig.gz |
1.1 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr10_13110.wig.gz |
1.1 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr11_13111.wig.gz |
1.3 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.bed.200_treat_afterfiting_chr12_13112.wig.gz |
1.3 Mb |
(ftp)(http) |
WIG |
| GSM756377_chd_K27me3.clean.fastq.gz |
434.5 Mb |
(ftp)(http) |
FASTQ |
| GSM756377_chd_K27me3.peaks.fa.gz |
16.8 Kb |
(ftp)(http) |
FA |
| GSM756377_chd_K27me3.soap.txt.gz |
486.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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