|
| Status |
Public on Feb 15, 2023 |
| Title |
AK58_DAP5_ATAC-seq_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Triticum aestivum endosperm at five days after fertilization
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: Endosperm
cultivar: AiKang58
|
| Treatment protocol |
Wheat endosperm was excised by removing the seed embryo at 5 and 9 days after fertilization. Wheat seed was collected at 15 and 20 days after fertilization.
|
| 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 |
| |
|
| 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.
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: peak files
|
| |
|
| Submission date |
Oct 04, 2022 |
| Last update date |
Feb 15, 2023 |
| 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) |
| GSE214737 |
Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development [ATAC-seq] |
| GSE214739 |
Chromatin accessibility landscapes revealed the subgenome-divergent regulation networks during wheat grain development. |
|
| Relations |
| BioSample |
SAMN31148880 |
| SRA |
SRX17915562 |
