NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8194301 Query DataSets for GSM8194301
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)
 
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
 
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

Supplementary file Size Download File type/resource
GSM8194301_jmj27_H3_0_R2.bigWig 60.5 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap
External link. Please review our privacy policy.