|
| Status |
Public on Nov 09, 2019 |
| Title |
H3K4me3-Col-0-rep2_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
Arabidopsis seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Arabidopsis seedlings
genotype: Col-0
|
| Growth protocol |
The Arabidopsis materials were all in the Columbia (Col-0) background and grown on Murashige and Skoog (MS) medium at 22°C with 16-h light/8-h dark (long-day conditions).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
DNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
ChIP-seq reads were aligned to the TAIR10 genome assembly using bowtie2 version 2.2.6 with parameters -k 1 -N 1 -p 40 --local -q
peaks were called using SICER v 1.1 with the following setting: window size 200, gap size 200, E-value 100, FDR 0.05
Genome_build: TAIR10
Supplementary_files_format_and_content: bw files were generated using deeptools bamCoverage with parameters --binSize 10 -p 30 --normalizeUsing RPKM --outFileFormat bigwig
|
| |
|
| Submission date |
Nov 08, 2019 |
| Last update date |
Nov 11, 2019 |
| Contact name |
xinjian He |
| E-mail(s) |
[email protected]
|
| Organization name |
National Institute of Biological Sciences
|
| Lab |
hexinjian
|
| Street address |
No. 7, zhongguancun life science park road, changping district
|
| City |
Beijing |
| ZIP/Postal code |
102206 |
| Country |
China |
| |
|
| Platform ID |
GPL23157 |
| Series (2) |
| GSE140136 |
Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis (ChIP-seq) |
| GSE140140 |
Intronic long noncoding RNAs activate host gene expression by affecting histone modification in Arabidopsis |
|
| Relations |
| BioSample |
SAMN13243091 |
| SRA |
SRX7119167 |
