|
| Status |
Public on Nov 28, 2022 |
| Title |
AK58_Root_ATAC-seq_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Triticum aestivum 2-weeks-old seedlings
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: roots
cultivar: AiKang58
|
| Treatment protocol |
The three tissues of wheat, including leaves, roots and shoot apices, were obtained after 2 weeks of growth. The 2-week-old seeding were vernalized at 4°C under 16h light/8h dark conditions for 30 days and 1.0 - 2.0 cm axillary buds were obtained from these vernalized seedings.
|
| Growth protocol |
16h light 22°C, 8h dark 19°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq libraries were prepared following the ATAC-seq protocol as previously described in (Lu et al. 2016)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Ta-R.final.bed
|
| Data processing |
Raw reads were trimmed with Trimmomatic v0.36, clean sequencing reads were mapped to the International Wheat Genome Sequencing Consortium (IWGSC) reference genome (version 1.0) using Bowtie2. Peak calling was performed using MACS2. A black list was first generated by using the control samples as input.The raw peaks were first called with MACS2 with the following parameter “--keep-dup all --nomodel --extsizes 150 --shift -75”; then split into 150bp bins with 50bp overlapping; bins passed filtering by a Tn5 integration site density cutoff were selected and merged with bedtools with “-d 150”; peaks overlapped with the blacklist peaks, or homologous to plant orgenella DNA (NCBI) were discard and the rest were considered as high-quality ACRs.
Genome_build: IWGSC RefSeq v1.0
Supplementary_files_format_and_content: peak files
|
| |
|
| Submission date |
Nov 12, 2021 |
| Last update date |
Nov 28, 2022 |
| Contact name |
Zefu Lu |
| E-mail(s) |
luzefu@live.com
|
| Organization name |
Institute of Crop Sciences
|
| Street address |
No.12 Zhongguancun South St.,Haidian District, Beijing, P.R.China
|
| City |
Beijing |
| State/province |
Haidian |
| ZIP/Postal code |
100081 |
| Country |
China |
| |
|
| Platform ID |
GPL25409 |
| Series (2) |
| GSE188696 |
Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [ATAC-seq] |
| GSE188724 |
Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat |
|
| Relations |
| BioSample |
SAMN23081888 |
| SRA |
SRX13121459 |
