|
| Status |
Public on Dec 01, 2022 |
| Title |
Adi-3_Input DNA |
| Sample type |
SRA |
| |
|
| Source name |
Adi-3
|
| Organism |
Brachypodium distachyon |
| Characteristics |
genotype/variation: Adi-3
tissue: young leaves
chip antibody: none
|
| Growth protocol |
Suitable materials were planted in the greenhouse ChIP-seq 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 different lines of Brachypodium species were performed Illumina sequencing. The CENH3 antibody is a rabbit polyclonal antiserum and was raised against the peptides: KDIQLARRISGHRGY. 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 different Brachypodium genomes 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 1 kb windows along the genome to make it comparable between different samples.
Genome_build: Bdistachyon_314_v3.0; Bhybridum_463_v1.0; Bstacei_316_v1.0
Supplementary_files_format_and_content: BED files contains the positions of mapped reads of the ChIP-seq.
|
| |
|
| Submission date |
Aug 30, 2020 |
| Last update date |
Dec 01, 2022 |
| Contact name |
Handong Su |
| E-mail(s) |
[email protected]
|
| 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 |
GPL17337 |
| Series (1) |
| GSE157143 |
Centromere evolution in Brachypodium genomes with different polyploid levels |
|
| Relations |
| BioSample |
SAMN15942358 |
| SRA |
SRX9036252 |
