|
Status |
Public on Sep 05, 2024 |
Title |
jmj27 H3 0 ChIP rep2 |
Sample type |
SRA |
|
|
Source name |
Leaves
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: Leaves ecotype: Col chip antibody: H3 genotype: jmj27 treatment: no UV-C time point: 0
|
Treatment protocol |
UV-C 3000J/m2
|
Growth protocol |
Plants were cultivated in vitro on solid GM medium [MS salts (Duchefa), 1% sucrose, 0.8% Agar-agar ultrapure (Merck), pH 5.8] and in a culture chamber under a 16 h light (light intensity ∼150 μmol m−2 s−1; 21°C) and 8 h dark (19°C) photoperiod
|
Extracted molecule |
genomic DNA |
Extraction protocol |
ChIP was performed upon sonication with the Bioruptor (Diagenode) using the Universal Plant Chip-seq Kit (Diagenode: C01010152) according manufacturers’ instructions Libraries were prepared with the MicroPlex Library Preparation Kit v3 (Diagenode: C05010001) and the 24 Dual indexes for MicroPlex Kit v3 (Diagenode-: C05010003)
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
NextSeq 2000 |
|
|
Data processing |
ChIP-seq analysis has been performed using the community curated nf-core ChIP-seq pipeline (version 1.2.2) with default parameters Reads have been mapped on the reference genome (TAIR10) and MACS2 was used to call H3K9me2 broad peaks using H3 as a reference, and an effective genome size of 119,481,543 bp Replicates were handled using the stringent irreproducibility discovery rate (IDR) framework and only peaks containing an IDR value superior or equal to a scaled IDR value of 540 were considered real, corresponding to an IDR of 0.05 Assembly: TAIR10 Supplementary files format and content: BigWig
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|
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Submission date |
Apr 09, 2024 |
Last update date |
Sep 05, 2024 |
Contact name |
Jean Molinier |
E-mail(s) |
Jean.Molinier@ibmp-cnrs.unistra.fr
|
Phone |
+33 (0) 3 67 15 53 12
|
Organization name |
IBMP-CNRS
|
Street address |
12 rue du General Zimmer
|
City |
Strasbourg |
ZIP/Postal code |
67084 |
Country |
France |
|
|
Platform ID |
GPL30821 |
Series (1) |
GSE263549 |
The histone demethylase JMJ27 acts during the UV-induced modulation of H3K9me2 landscape and facilitates photodamage repair |
|
Relations |
BioSample |
SAMN40895907 |
SRA |
SRX24198210 |