|
| Status |
Public on Mar 27, 2024 |
| Title |
H3K9K14Ac, HDC1 KO mutant, control medium |
| Sample type |
SRA |
| |
|
| Source name |
seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
age: 3 days old
tissue: seedlings
genotype: HDC1 KO mutant
treatment: control
chip antibody: Anti-H3K9K14Ac (Diagenode pAb-005-050 )
|
| Treatment protocol |
Sterilized seeds were then sown on 1/2 MS 1% sucrose plates with or without 100 mM NaCl. At day 3 after sowing the seeds were harvested and and snap-frozen with liquid N2.
|
| Growth protocol |
Seeds were sterilised with 50% bleach solution, wash with dH2O water three times and stored at 4C for two days.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP assays were performed on 2g of tissue as described previously with minor modifications (Sani et al., 2013). A Bioruptor sonicator (Diagenode, B01020001) was used to shear the chromatin using the following settings: 20 cycles x 30 sec ON, 30 sec OFF at high power.
ChIP-seq libraries were prepared using the NEBNext Ultra DNA Prep Kit according to the manufacturer’s protocol, size selected with SPRIselect Beads and amplified by PCR.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
hdc1-1 AC ctrl
|
| Data processing |
Fastq files were generated with bcl2fastq v.1.8.4 Illumina software
The raw fastq files were pre-processed to trim the 3’ end adapter and to trim the low quality reads using Cutadapt (version 1.9.2) and Sickle (version 0.940; flags -q 10 -l 54), respectively.
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie version 0.12.7. Only uniquely mapping reads with at most two mismatches in the first 54 bp were retained.
The alignment files were then sorted, and the duplicated reads of the same orientation were removed using Samtools (version 0.1.19). The locations of the mapped ChIP-seq reads were shifted in the 3'end direction by half of the sample-specific mean fragmernt length to represent the centres of sequenced fragments. Reads were then counted in 200 bp long windows and resulting raw counts stored in WIG files.
For each sample the aligned reads positions were shifted in the 3’end direction by half of the sample-specific mean fragment length to represent the centres of sequenced fragments, counted in 200-bp long windows using Sicer (version 1.03)(Zang et al., 2009) and resulting profiles stored in WIG files,
Assembly: TAIR10
Supplementary files format and content: WIG
|
| |
|
| Submission date |
Jun 13, 2022 |
| Last update date |
Mar 27, 2024 |
| Contact name |
Pawel Herzyk |
| E-mail(s) |
[email protected]
|
| Phone |
00441413303180
|
| Organization name |
University of Glasgow
|
| Department |
College of Medical, Veterinary and Life Sciences
|
| Lab |
Glasgow Polyomics
|
| Street address |
Wolfson Wohl Cancer Research Centre, Garscube Estate
|
| City |
Bearsden |
| ZIP/Postal code |
G61 1QH |
| Country |
United Kingdom |
| |
|
| Platform ID |
GPL19580 |
| Series (2) |
| GSE206054 |
Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process [ChIP-Seq] |
| GSE206055 |
Histone Deacetylase Complex 1 moderates stress responsiveness of germinating seeds via a histone-1-dependent process |
|
| Relations |
| BioSample |
SAMN29019756 |
| SRA |
SRX15695623 |
