|
|
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Jul 22, 2024 |
Title |
ATAC-Seq Leaf_rep1 |
Sample type |
SRA |
|
|
Source name |
Leaf
|
Organism |
Triticum aestivum |
Characteristics |
tissue: Leaf
|
Growth protocol |
Wheat (Triticum aestivum; BBAADD, 2n = 6x = 42) cultivar AK58 was used in our study. Materials with no vernalization were taken from plants grown 2 weeks (day for 16h at 22°C, night for 8h at 19°C) after germination. Materials with vernalization were taken from plants planted in greenhouse after vernalization for 1 mouth in cold chamber (4℃, 16 h light/8 h dark) and grew in green house (day for 16h at 22°C, night for 8h at 19°C) for 1 day.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
none provided
|
|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
We used fastp v0.21.0 for data quality control and Bowtie v2.3.5.1 to align reads to wheat reference genome (bowtie2 -X 1000 --very-sensitive). SAMtools v1.3.1 was used to sort and filter bam (samtools -q 10), Picard v2.16.0 to remove clonal duplicate, and MACS2 v 2.2.6 to call peak(macs2 --keep-dup all --nomodel --extsizes 150 --shift -75). All the raw peaks were split into 150 bp bins with 50 bp overlapping, filtered by Tn5 integration site density, and merged by bedtools with “-d 200”. Peaks overlapped with input and aligned to plant chloroplast DNA (NCBI) were discard, which guaranteed ACRs we identified were high-quality ACRs. Assembly: ChineseSpring v1.1 Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
|
|
|
Submission date |
May 12, 2023 |
Last update date |
Jul 22, 2024 |
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) |
GSE232424 |
Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ATAC-Seq) |
GSE232430 |
Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat |
|
Relations |
BioSample |
SAMN35063625 |
SRA |
SRX20313527 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7333164_Leaf.peak.bed.gz |
1.0 Mb |
(ftp)(http) |
BED |
GSM7333164_Leaf_rep1.bw |
222.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
|