|
| Status |
Public on Nov 28, 2022 |
| Title |
SPL11A |
| Sample type |
SRA |
| |
|
| Source name |
Triticum aestivum 2-weeks-old seedlings
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: leaves
cultivar: AiKang58
treatment: Magne-HALO Tag beads (Promega, G7282)
|
| Treatment protocol |
Full length TF was cloned into pIX-Halo vector, the HALO-SPL protein was generated using 500 ng of pIX-HALO-SPL plasmid and the TNT SP6 Coupled Reticulocyte Lysate System (Promega, L4600) according to the manufacturer’s protocol. The reaction was then incubated with 10 μL of Magne-HALO Tag beads (Promega, G7282) for 1 h at 25 °C in 1× PBS with 0.005% Nonidet P-40 (PBST). Bound protein was washed five times with PBST and subsequently treated with DNaseI. The DNA-free HALO-SPL protein was incubated with 500 μg of ultrasonicated genomic DNA library (200~800 bp) for 1 h at 25 °C. The beads were then washed eight times with PBST and incubated with 1μl Tn5 transposomes in 40 μl of tagmentation buffer (10 mM TAPS-NaOH ph 8.0, 5 mM MgCl2) at 55°C for 10 minutes. The DNA were recovered by NEB Monarch™ DNA Cleanup Kit (T1030L) and then amplified using Phusion DNA polymerase for 10-13 cycles. Amplified libraries were purified with AMPure beads to remove primers.
|
| Growth protocol |
16h light 22°C, 8h dark 19°C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
genomic DNA
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
SPL11A.final.bed
|
| Data processing |
Library strategy: DAP-seq
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. Raw peaks were first identified with MACS2 with the following parameter with the following parameter “--keep-dup all --nomodel --extsizes 150”; then split into 150bp bins with 50bp overlapping; bins passed filtering using a reads 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 binding peaks.
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) |
| GSE188699 |
Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat [DAP-seq] |
| GSE188724 |
Low-affinity SPL binding sites contribute to subgenome expression divergence in allohexaploid wheat |
|
| Relations |
| BioSample |
SAMN23082130 |
| SRA |
SRX13121521 |
