|
| Status |
Public on Feb 18, 2018 |
| Title |
H3.3swap-2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype: Columbia-0
tissue: leaf
genotype: H3.3H87S L90A mutation
|
| Growth protocol |
Arabidopsis plants were grown on soil at 21 degree under continuous light for 3 weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP genomic DNA protocols are followed by Zhong et al., Nat Struct Mol Biol, 2012, 19:870-850
ChIP library was construbuted by using the Ovation Ultralow Library Kit (NuGen, Part No. 0330)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Genomic DNA isolated from immnuoprecipitated chromatin using FLAG antibody
H3.3H87S L90A mutation replicate 2
|
| Data processing |
ChIPseq reads were filtered for average QC score>30. Reads were mapped with Bowtie2 to the TAIR10 genome, with default parameters. Reads mapping to identical positions in the genome were collapsed into one read.
Samtools and Bedtools were used to generate bed file and bedGraph file
Bigwig file generated by UCSC "bedGraphToBigWig" scipts
Genome_build: TAIR10 for Arabidopsis
Supplementary_files_format_and_content: bigwig file
|
| |
|
| Submission date |
Jan 05, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuehua Zhong |
| Organization name |
Wisconsin Institute for Discovery
|
| Department |
Epigenetics
|
| Street address |
330 N. Orchard St.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL13222 |
| Series (1) |
| GSE93223 |
Plant-specific histone residue F41 restricts H3.1 distribution in heterochromatin |
|
| Relations |
| BioSample |
SAMN06209150 |
| SRA |
SRX2467601 |
