 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Dec 31, 2019 |
| Title |
FP3_ATAC_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Fertility male of WXS at meiosis period
|
| Organism |
Oryza sativa |
| Characteristics |
line: Wuxiang S (WXS)
genotype: photo-thermosensitive genic male sterile (PTGMS) rice line
tissue: panicle
period: meiosis
|
| Treatment protocol |
Young panicles were collected and were immediately frozen in liquid nitrogen. All collected samples were ground into fine powder for ChIP-seq, ATAC-seq and RNA-seq experiments.
|
| Growth protocol |
The rice PTGMS line WXS (O. sativa ssp. indica) were grown in the paddy field of Wuhan University (30.35°N, 114.33°E), Wuhan, China, in summer. From 20 July to 30 August 2016, the average temperatures were? , with a 14h light/10 h dark photoperiod, which caused WXS male sterility (WXS(S)). When panicle length reached ~ 1 cm (before the stages of early premeiosis), half of the plants were transferred to growth chamber at an average temperature of 22°C with a 14h light/10h dark photoperiod and 77% relative humidity, ensuring the illumination, humidity values and other environment factors in the growth chamber close to the natural condition as far as possible, which could make WXS convert into male fertility (WXS(F))
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tn5 Transposase treatment (Using the Illumina Nextera kit) was performed on the intact nuclei isolated by Plant Nuclei Isolation/Extraction Kit (CELLYTPN1, sigma) from each sample, followed by isolation of fragmented genomic DNA using the Qiagen PCR purification kit. Purified transposase-fragmented DNAs were converted to sequencing libraries through a limited number of PCR cycles using indexed primers. Total RNA of WXS was isolated using TRIzol reagent (Invitrogen) according to the manufacturer's instructions. Chromatin from panicle of WXS was immunoprecipitated with antibodies against H3K4me2 and H3K9ac. The eluted ChIP DNA was used to generate Illumina sequencing libraries following the manufacturer's protocol.
The genomic fragments of Tn5, RNA libraries and ChIP-ed DNA were separately prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Raw reads of ATAC-seq, ChIP-seq and RNA-seq were separately aligned to the O.sativa Nipponbare release 7 of the MSU Rice Genome Annotation Project reference using Bowtie2, SOAP2 aligner and HISAT2 with default parameters.
Mapped reads were filtered to remove those mapping to organelle genomes, and reads with a mapping quality score of q>2 were retained for further analysis.
Peaks of ATAC-seq and ChIP-seq were identified using the MACS and SICER
Genome_build: MSU7
Supplementary_files_format_and_content: bed file were generated by MACS, scores represent -10*log10(pvalue); wig files were generated using SICER, Scores represent probability；tab-delimited text files include RPKM values for each sample.
|
| |
|
| Submission date |
May 07, 2018 |
| Last update date |
Dec 31, 2019 |
| Contact name |
jin jing |
| E-mail(s) |
jinjing1130@whu.edu.cn
|
| Phone |
13419585813
|
| Organization name |
Wuhan University
|
| Department |
College of Life Sciences
|
| Lab |
State Key Laboratory of Hybrid Rice
|
| Street address |
Wuhan, Hubei Province, P.R.China
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL23013 |
| Series (1) |
| GSE114090 |
ATAC-seq profiling of open chromatin with global epigenetic and transcriptional trends in two-line hybrid rice |
|
| Relations |
| BioSample |
SAMN09080735 |
| SRA |
SRX4047136 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3132600_FP3_ATAC_rep2_peaks.bed.gz |
880.8 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
