|
| Status |
Public on Dec 25, 2023 |
| Title |
α-RFP, HAC1:mCherry, -INA, MNase, rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: Seedlings
genotype: HAC1:mCherry transgenic line
developmental stage: 4-week-old
treatment: Distilled water
time: 12 hours
chip antibody: RFP-trap agarose (ChromoTek, rta-20)
|
| Treatment protocol |
300 μM INA or distilled water was sprayed onto 4-week-old seedlings and then the seedlings were incubated for 12 hours.
|
| Growth protocol |
Plants were grown on Murashige and Skoog basal medium under 8-hour light / 16-hour dark photoperiod for 4 weeks.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Seedlings were fixed with formaldehyde and then qeunched with glycine. After isolating nuclei from crosslinked sample, chromatin was fragmentated by sonication or micrococcal nuclease (MNase) treatment. NPR1:GFP or HAC1:mCherry proteins within the chromatin were immunoprecipitated by using anti-GFP or anti-RFP antibody, respectively. Genomic DNAs co-immunoprecipitated with NPR1:GFP or HAC1:mCherry were purified and used for sequencing.
ChIP-seq libraries were prepared by using NEBNext® Ultra™ II DNA Library Prep with Sample Purification Beads (NEB, E7103) and NEBNext® Multiplex Oligos for Illumina® (NEB, E7335). 10 ng of DNA per sample was used for library-construction reaction. Prepared libraries were amplified by 9 cycles of PCR. For DNA samples collected from ChIP involving MNase digestion, sonication was additionally performed at mild condition before library preparartion.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
α-RFP_HAC1:mCherry-INA_MNase_rep1
|
| Data processing |
ChIP-seq reads were trimmed by using Trimmomatic v0.38 with options of “-phred33 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36”.
Trimmed ChIP-seq reads were aligned to TAIR10 Arabidopsis genome by using Bowtie version 1.1.2 with options of “-S --best --strata -X 500 -m 1 --chunkmbs 500”.
BAM files were deduplicated by using Picard markDuplicate v.1.118.
Deduplicated BAM files were converted to bedgraph format by using bedtools genomecov v2.27.0.
Bedgraph files were converted to bigwig files by using bedGraphToBigWig v4.
Assembly: Arabidopsis thaliana (TAIR10)
Supplementary files format and content: Bigwig
|
| |
|
| Submission date |
Aug 11, 2022 |
| Last update date |
Dec 25, 2023 |
| Contact name |
Se-Hun Yun |
| E-mail(s) |
leolivine@gmail.com
|
| Organization name |
Seoul National Univ.
|
| Street address |
1 Gwanak-ro, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL21785 |
| Series (1) |
| GSE211047 |
Genome-wide analyses of NPR1 and HAC1 direct targets in Arabidopsis |
|
| Relations |
| BioSample |
SAMN30265382 |
| SRA |
SRX17033312 |
