NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM7809255 Query DataSets for GSM7809255
Status Public on Oct 18, 2023
Title GFP-NHS-r2
Sample type SRA
 
Source name seedlings
Organism Arabidopsis thaliana
Characteristics tissue: seedlings
chip antibody: anti-GFP
genotype: pHSP21::HTR5::eGFP::3'HSP21
treatment: No Heat Shock
Treatment protocol HS treatments were performed on 5 d-old seedlings by a treatment of 37°C for 60 min, 22°C for 90 min and 44°C for 45 min.
Growth protocol Plants were grown on GM medium (1% glucose) under a 16/8 h light/dark cycle at 23/21°C.
Extracted molecule genomic DNA
Extraction protocol Seedlings were crosslinked under vacuum in PBS buffer with 1 % (w/v) formaldehyde for 10 min on ice. Chromatin was extracted as described previously (Kaufmann et al., 2010)⁠. Chromatin was fragmented using a Bioruptor (Diagenode – 20 cycles 30sec on/30sec off). For single ChIP, chromatin was immunoprecipitated overnight at 4°C with IgG (ThermoFisher 026102), anti-panH3 (Diagenode C15200011) or anti-GFP (Chromotek PABG1) antibodies. Antibody-chromatin complexes were purified with Dynabeads (ThermoFischer 10002D) and successively washed with low salt (150 mM NaCl, 1 % (v/v) Triton X-100), high salt (500 mM NaCl, 1 % (v/v) Triton X-100), LiCl buffer (250 mM LiCl, 1 % (v/v) NP-40) and TE buffer. Chromatin was eluted with single ChIP elution buffer (1 % (w/v) SDS, 0.1 M NaHCO3).
ChIP DNA was generated and libraries were prepared using NEBNext Ultra II FS DNA Library preparation kit (NEB E7645). Quality control was performed with TapeStation D1000 ScreenTape system (Agilent) and a Qubit fluorometer (Thermo Fisher).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Data processing Reads were mapped against the Arabidopsis thaliana reference genome (TAIR10) using bwa mem.
Duplicates were removed using samtools markdup
Reads for biological replicates were merged. Both individual samples and merged replicates were processed as follows.
Normalized coverage tracks were generated using deeptools bamCoverage (--binSize 10 --normalizeUising RPGC --extendReads). Artifactual regions identified using Greenscreen, chloroplast and mitochondria sequences were excluded.
Assembly: Arabidopsis thaliana TAIR10
Supplementary files format and content: Normalized coverage files in bigWig format
 
Submission date Sep 28, 2023
Last update date Oct 18, 2023
Contact name Isabel Bäurle
E-mail(s) isabel.baeurle@uni-potsdam.de
Phone +49 331 9772647
Organization name Universität Potsdam
Department Institut für Biochemie und Biologie
Street address Karl-Liebknecht-Str. 24-25
City Potsdam
ZIP/Postal code 14476
Country Germany
 
Platform ID GPL19580
Series (1)
GSE218234 Histone retention preserves epigenetic marks during heat stress-induced transcriptional memory
Relations
BioSample SAMN37576644
SRA SRX21915108

Supplementary file Size Download File type/resource
GSM7809255_GFP-NHS-r2.SeqDepthNorm.bw 42.1 Mb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap