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| Status |
Public on Apr 09, 2018 |
| Title |
rep2 o11 ChIP |
| Sample type |
SRA |
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| Source name |
kernal
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| Organism |
Zea mays |
| Characteristics |
tissue: kernel
developmental stage: 15 DAP
genotype: mutant (o11/o11)
chip antibody: anti-O11
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Dissected 15 DAP kernels was immediately cross-linked in buffer containing 1% formaldehyde on ice under vacuum for 15 min, released the vacuum and reapplied for another 14 min. Fixation was stopped by adding 1.25M glycine. The cross-linked kernels were dried and ground into powder in liquid nitrogen, followed by nuclear isolation and sonication. Protein A-agarose beads (Millipore) and Antibody against O11 were used to precipitate the DNA. The precipitated DNA was digest by proteinase K and recovered using a QIAquick PCR purification kit (Qiagen) and analyzed by qPCR
[ChIP antibody anti-O11 preparation] Prepared by Abclonal of China company. The full-length O11 cDNA was cloned into the EcoR I and Xho I sites of the pET-32a vector (Novagen) and transformed into BL21. The 6xHis fusion recombinant O11 protein was purfied with the ÄKTA purfication system using a 1 mL HisTrap FF crude column (GE Healthcare). Then the antibody was prepared in rabbits by Abclonal of China company.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq ChIP Sample Prep Kit (Catalog# IP-202-1012). ChIP DNA samples were subjected to end repair and A-base addition, followed by ligation with adapters. Then libraries werebarcoded to allow multiplexed sequencing.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
rep2 ChIP control
rep2_peaks.txt
rep2_summits.bed
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| Data processing |
CASAVA1.8.2 (Illumina) were used for image analysis and base calling.
Raw fastq data were trimmed using SolexaQA v2.5 program with Q20 (Phred score) and L40 (Length).
Cleaned data were then mapped to the maize reference genome (AGPv3.26, http://plants.ensembl.org/) using Bowtie2 (v2.3.2) with default parameters and allowing unique reads only.
Peak calling was performed separately for each biological replicate using MACS2 (v2.1.0) (band width = 300；model fold = [10, 30]; qvalue cutoff = 0.01)
UCSC bedGraph files were created at 1bp resolution and normalized to total alignable reads (reads-per-million).
Genome_build: Ensembl plants release-26 zea_mays
Supplementary_files_format_and_content: tab-delimited text files include information about called peaks. bed files include the peak summits locations for every peak.
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| Submission date |
Jul 31, 2017 |
| Last update date |
Apr 09, 2018 |
| Contact name |
Liming Xu |
| E-mail(s) |
17602190375@163.com
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| Phone |
17602190375
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| Organization name |
Shanghai University
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| Street address |
333 Nanchen Road
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| City |
Shanghai |
| ZIP/Postal code |
200444 |
| Country |
China |
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| Platform ID |
GPL17628 |
| Series (1) |
| GSE102051 |
Genome-wide characterization of cis-acting DNA targets of Opaque11 in maize |
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| Relations |
| BioSample |
SAMN07427120 |
| Supplementary data files not provided |
| Raw data provided as supplementary file |
| Processed data are available on Series record |
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