|
| Status |
Public on Dec 21, 2019 |
| Title |
F3-600 |
| Sample type |
SRA |
| |
|
| Source name |
maize
|
| Organism |
Zea mays |
| Characteristics |
tissue: young leaves
genotype/variation: F3-600
chip antibody: CENH3
|
| Growth protocol |
Suitable materials were planted in the greenhouse or in the field for RNA-seq and ChIP-bisulfite experiments.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Extracted nuclei were digested with micrococcal nuclease (Sigma-Al drich) for ChIP experiments using the maize CENH3 antibody.The ChIP-enriched DNAs of B73, F3-152 and F3-600 were performed Illumina sequencing. The maize CENH3 is a rabbit polyclonal antiserum and was raised against the peptides: C-RPGTVALREIRKYQKS; STSATPERAAGTGGR-C. Keyhole limpet hemocyanin (KLH)-conjugated peptide was used to immunize rabbits.
ChIP libraries were prepared according to standard Illumina's instructions.180-400 bp fragments (contained the joint) were selected by gel extraction.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Basecalls performed using Illumina CASAVA.
Raw reads from ChIP-seq data were mapped to the B73 RefGen_v4 genome using bwa mem with the default parameters.
The mapped reads with MAPQ values >= 20 as uniquely mapping for further analysis.
RPM values were calculated with 10 kb windows along the genome to make it comparable between different samples.
Genome_build: Maize B73 RefGen_v4
Supplementary_files_format_and_content: BED files contains the positions of mapped reads of the ChIP-seq.
|
| |
|
| Submission date |
Dec 21, 2018 |
| Last update date |
Dec 22, 2019 |
| Contact name |
Handong Su |
| E-mail(s) |
shandong@mail.hzau.edu.cn
|
| Phone |
+86-18810795796
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
No.1,Shizishan Street ยท Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL15463 |
| Series (1) |
| GSE124242 |
De novo formation in maize from irradiated materials |
|
| Relations |
| BioSample |
SAMN10623927 |
| SRA |
SRX5172987 |
