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| Status |
Public on Dec 25, 2023 |
| Title |
Genome-wide analyses of NPR1 and HAC1 direct targets in Arabidopsis |
| Organism |
Arabidopsis thaliana |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Genome-wide direct targets of Arabidopsis NPR1 and HAC1 were identified by chromain immunoprecipitation followed by sequencing (ChIP-seq). For the study, we used Arabidopsis expressing NPR1:GFP or HAC1:mCherry under native NPR1 or HAC1 promoter, respectively. To identify direct targets both under salicylic acid-treated and untreated conditions, we performed ChIP-seq by using 2,6-dichloroisonicotinc acid (INA; synthetic SA analog)-treated and untreated NPR1:GFP or HAC1:mCherry transgenic Arabidopsis plants.
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| Overall design |
For the rep1&2 NPR1:GFP ChIP-seq, chromatin was digested by sonication and immunoprecipitation (IP) was performed in condition containing 1% sodium dodecyl sulfate (SDS). For the rep3&4 NPR1:GFP ChIP-seq, chromatin was digested by micrococcal nuclease (MNase) treatment and IP was performed in condition containing 0.02% SDS. For the rep1&2 HAC1:mCherry ChIP-seq, chromatin digestion and IP were performed as described for the rep3&4 NPR1:GFP ChIP-seq. Samples were treated either with INA (+INA) or water (-INA) and incubated for 12 hours before harvesting. Columbia-0 (Col) was used as a non-transgenic wild-type control.
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| Contributor(s) |
Yun S, Khan IU, Noh B, Noh Y |
| Citation(s) |
38261978 |
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| Submission date |
Aug 11, 2022 |
| Last update date |
Mar 25, 2024 |
| Contact name |
Se-Hun Yun |
| E-mail(s) |
leolivine@gmail.com
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| Organization name |
Seoul National Univ.
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| Street address |
1 Gwanak-ro, Gwanak-gu
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| City |
Seoul |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platforms (1) |
| GPL21785 |
Illumina HiSeq 4000 (Arabidopsis thaliana) |
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| Samples (24)
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| GSM6448376 |
Input, NPR1:GFP, +INA, Sonication, rep1 |
| GSM6448377 |
α-GFP, Col, -INA, Sonication, rep1 |
| GSM6448378 |
α-GFP, NPR1:GFP, -INA, Sonication,rep1 |
| GSM6448379 |
α-GFP, NPR1:GFP, +INA, Sonication, rep1 |
| GSM6448380 |
Input, NPR1:GFP, +INA, Sonication, rep2 |
| GSM6448381 |
α-GFP, Col, -INA, Sonication, rep2 |
| GSM6448382 |
α-GFP, NPR1:GFP, -INA, Sonication, rep2 |
| GSM6448383 |
α-GFP, NPR1:GFP, +INA, Sonication, rep2 |
| GSM6448384 |
Input, NPR1:GFP, +INA, MNase, rep3 |
| GSM6448385 |
α-GFP, Col, -INA, MNase, rep3 |
| GSM6448386 |
α-GFP, NPR1:GFP, -INA, MNase, rep3 |
| GSM6448387 |
α-GFP, NPR1:GFP, +INA, MNase, rep3 |
| GSM6448388 |
Input, NPR1:GFP, +INA, MNase, rep4 |
| GSM6448389 |
α-GFP, Col, -INA, MNase, rep4 |
| GSM6448390 |
α-GFP, NPR1:GFP, -INA, MNase, rep4 |
| GSM6448391 |
α-GFP, NPR1:GFP, +INA, MNase, rep4 |
| GSM6448392 |
Input, HAC1:mCherry, +INA, MNase, rep1 |
| GSM6448393 |
α-RFP, Col, -INA, MNase, rep1 |
| GSM6448394 |
α-RFP, HAC1:mCherry, -INA, MNase, rep1 |
| GSM6448395 |
α-RFP, HAC1:mCherry, +INA, MNase, rep1 |
| GSM6448396 |
Input, HAC1:mCherry, +INA, MNase, rep2 |
| GSM6448397 |
α-RFP, Col, -INA, MNase, rep2 |
| GSM6448398 |
α-RFP, HAC1:mCherry, -INA, MNase, rep2 |
| GSM6448399 |
α-RFP, HAC1:mCherry, +INA, MNase, rep2 |
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| Relations |
| BioProject |
PRJNA868735 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE211047_RAW.tar |
4.0 Gb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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