|
| Status |
Public on Oct 18, 2023 |
| Title |
GFP-4h-r2 |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: seedlings
chip antibody: anti-GFP
genotype: pHSP21::HTR5::eGFP::3'HSP21
treatment: HS+4h
|
| 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 |
SAMN37576647 |
| SRA |
SRX21915105 |
