|
| Status |
Public on Jan 31, 2024 |
| Title |
LH2 IP |
| Sample type |
SRA |
| |
|
| Source name |
leaf
|
| Organism |
Brassica rapa var. parachinensis |
| Characteristics |
tissue: leaf
chip antibody: Anti-GFP antibody (ab290, Abcam)
cell type: mesophyll cell
genotype: BrJMJ18PraOX
treatment: Low temperature (21C)
|
| Growth protocol |
Par plants grown under 21℃ for 5 weeks or 4 weeks following 1 weeks under 28℃ were used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
1.5 g samples were washed twice in cold phosphate-buffered saline (PBS), cross-linked with 1% formaldehyde for 10 minutes at room temperature, and then quenched by the addition of glycine (125 mmol/L final concentration). Afterwards, samples were lysed and chromatin was obtained on ice. Chromatin was sonicated to get soluble sheared chromatin (average DNA length of 200–500 bp).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
BrJMJ18Par overexpressing Par grown und 21℃. Anti-GFP IP
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.1.0 with the significance cut-off q-value <=0.01
Assembly: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Supplementary files format and content: ZIP
Supplementary files format and content: annotation call_peak GO_KEGG motif
|
| |
|
| Submission date |
Jan 29, 2023 |
| Last update date |
Jan 31, 2024 |
| Contact name |
Peirong Li |
| E-mail(s) |
lprdream@126.com
|
| Organization name |
Beijing Academy of Agricultural and Forestry Sciences
|
| Street address |
Zhanghualu No.50
|
| City |
Beijing |
| State/province |
Beijing |
| ZIP/Postal code |
100097 |
| Country |
China |
| |
|
| Platform ID |
GPL33070 |
| Series (1) |
| GSE223969 |
ChIP-seq using BrJMJ18-OX Par plants under NC and HS conditions |
|
| Relations |
| BioSample |
SAMN32954037 |
| SRA |
SRX19210631 |
