|
| Status |
Public on Jan 19, 2024 |
| Title |
PHYB-GFP/AbCDE, 5 minutes, rep 1 |
| Sample type |
SRA |
| |
|
| Source name |
6-day-old etiolated seedlings (at 17 °C). Following a red light pulse at 50 µmol m-2 s-1 fluence rate for 5 min.
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 6-day-old etiolated seedlings (at 17 °C). Following a red light pulse at 50 µmol m-2 s-1 fluence rate for 5 min.
genotype: PHYB-GFP/AbCDE
treatment: red light pulse at 50 µmol m-2 s-1 fluence rate for 5 min.
|
| Treatment protocol |
Following a red light pulse at 50 µmol m-2 s-1 fluence rate for 5 min, seedlings were fixed in 1 % (v/v) formaldehyde solution.
|
| Growth protocol |
Surface sterilised seeds were sowed on half-strength MS media and stratified for 3 days at 4 °C. Germination was induced by white light treatment for 6 h, then the plates were incubated in the darkness for 6 days at 17 °C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ChIP protocol by Werner Aufsatz (https://www.epigenome-noe.net/researchtools/protocol.php_protid=13.html) was applied with the following modifications. Chromatin samples were sonicated on ice six times for 10 s using a Vibra Cell sonicator (SONICS & MATERIALS Inc., Danbury, CT, USA) at 10% power. Sonicated and diluted chromatin samples were pre-cleared by 20 µl (bed volume) of binding control agarose beads (Chromotek GmbH, Germany) for 1 h at 4 °C. Chromatin was precipitated using 12.5 µl (bed volume) of GFP-Trap agarose beads (Chromotek GmbH, Germany) for 16 h at 4 °C. Precipitated chromatin was eluted from the beads, de-crosslinked and DNA was extracted using the NucleoSpin® Gel and PCR Clean-up kit (Macherey-Nagel, Düren, Germany) with Buffer NTB (Macherey-Nagel, Düren, Germany).
Library preparation was performed using NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) along with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2, New England BioLabs) according to the manufacturer’s protocol. Final libraries were quality checked using D1000 ScreenTape and Reagents on TapeStation 2200 (all from Agilent); quantification was performed using Qubit dsDNA BR Assay kit (Thermo Fischer Scientific). Sequencing was performed on Illumina NextSeq 1000 instrument.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequence reads were trimmed using TrimmomaticPE.0.39 with this parameters:ILLUMINACLIP:TruSeq3-PE-2.fa:2:30:10, LEADING:5 TRAILING:5, SLIDINGWINDOW:5:20, MINLEN:50.
Quality controlled reads (FastQC), were mapped to reference genom using bowtie v2.4.2
PCR duplicates were identified with PicardTools MarkDuplicates v.2.24.
Peaks were called using MACS2 v.2.2.7.1 with the significance cutoff <=0.05 with 147 base pair exact size.
Assembly: TAIR10
Supplementary files format and content: bw, narrowPeak
|
| |
|
| Submission date |
Jan 15, 2024 |
| Last update date |
Jan 19, 2024 |
| Contact name |
Gabor Grezal |
| E-mail(s) |
grezal.gabor@gmail.com
|
| Phone |
0036303063101
|
| Organization name |
Biological Research Centre
|
| Department |
Institute of Biochemistry
|
| Lab |
Balázs Papp Laboratory
|
| Street address |
Temesvári krt. 62.
|
| City |
Szeged |
| State/province |
Csongrád |
| ZIP/Postal code |
6701 |
| Country |
Hungary |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE253236 |
Phytochrome C and Low Temperature Promote the Expression and Red Light Signaling of Phytochrome D |
|
| Relations |
| BioSample |
SAMN39442794 |
| SRA |
SRX23218474 |
