|
| Status |
Public on Jun 20, 2024 |
| Title |
hda6 Gen3_12-hr_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
leaf at bolting stage
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: leaf at bolting stage
cell line: Col-0
genotype: hda6(F4)
treatment: 12-hr, no heat
|
| Treatment protocol |
For the heat stress experiment, plants were grown at normal condition (22/20 ⁰C) for 10 days for germination. Then, treatment plants were moved to 28/26 ⁰C.
|
| Growth protocol |
Seeds were stratified in water at 4 ⁰C for 2 - 3 d and sown on soil and grown in growth chambers with 22/20 ⁰C with 12-hr or 16-hr daylength and 120 − 150 μmol m−2 s−1 light.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted with NucleoSpin Plant II Kit (Macherey-Nagel, Germany).
Library was constructed and sequenced as paired-end 100-bp for the Batch 1 (WT_12h, cue1_12h, hda6_12h) and paired-end 150-bp for other batches
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Data processing |
Raw whole-genome bisulfite sequencing data was trimmed using Trim Galore! (v0.6.6) with Cutadapt (v2.8)
Aligned to the TAIR10 reference genome using Bismark (v0.23.1) with Bowtie 2 (v3.5.1) and Samtools (v1.10).
Assembly: TAIR10
Supplementary files format and content: Each row contains read count data with <chromosome> <position> <strand> <count methylated> <count unmethylated> <C-context> <trinucleotide context> in txt format
|
| |
|
| Submission date |
Jun 17, 2024 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Ha Eun Jeh |
| E-mail(s) |
huj181@psu.edu
|
| Phone |
8148268075
|
| Organization name |
Penn State University
|
| Street address |
362 Frear N Bldg
|
| City |
University Park |
| State/province |
PA |
| ZIP/Postal code |
16802 |
| Country |
USA |
| |
|
| Platform ID |
GPL34608 |
| Series (1) |
| GSE270032 |
Plastid signaling triggers HDA6-mediated epigenetic programs during environmental sensing in plants [Bisulfite-seq] |
|
| Relations |
| BioSample |
SAMN41879663 |
| SRA |
SRX24951931 |
