 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 04, 2020 |
| Title |
ZH11-WT_ATACseq_1 |
| Sample type |
SRA |
| |
|
| Source name |
seedling root from ZH11-WT, under normal condition, replicate1
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: ZH11-WT root
developmental stage: 4-leaf stage
treatment: normal
|
| Treatment protocol |
Seedlings were grown in normal condition (28°C during day light, 22°C at night). For drought stress treatment, the seedlings were deprived from water supply for three hours before sampling.
|
| Growth protocol |
Seedling (25-day-old) roots from hydroponic culture were harvested for genomic DNA or total RNA extraction.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Seedling roots were splintered into pieces and nuclei were isolated using ice-cold buffer (15 mM Tris-HCl pH7.5, 20 mM NaCl, 80 mM KCl, 0.5 mM spermine, 3 mM DTT, 0.2% TritonX-100) then filtered with a 100 μm filter. Nuclei were stained with DAPI and loaded into a flow cytometer (Becton Dickinson FACSCalibur). Nuclei were sorted and collected 200,000 in a 1.5-ml centrifuge tube containing lysis buffer. Nuclei were resuspended in 1× TD buffer (Illumina) and 4 μL Tn5 transposes (Illumina) were added. The transposition reaction was performed in a thermocycler by centrifugation at 300 rpm for 30 min at 37 °C, and directly purified the DNA with a TaKaRa MiniBEST DNA Fragment Purification Kit (Potter et al., 2018). DNA libraries were amplified for a total of eleven cycles as described (Buenrostro et al., 2013) and purified the product with AMPure® XP Beads Kit.
Library construction was performed by Novogene Inc (Tianjin, China) accroding to the standard protocol of Illumina.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
ZH11_ATACseq_pooled.rpgc.bw
|
| Data processing |
For RNA-seq analysis, the raw reads were filtered by fastp with the parameter “-q 30” (Chen et al., 2018) and checked by FastQC v0.11.8 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) to ensure the exclusion of adaptor and low quality sequences. The resulting reads were mapped to rice reference genome RGAP 7 (Kawahara et al., 2013) using STAR v1.5.2 (Dobin et al., 2013) with default parameters. The alignments were further filtered (-b -f 2 -F 524 -q 5), sorted and indexed by SAMtools v1.9 (Li et al., 2009) before the transcripts were assembled and count by StringTie v1.3.6 (Pertea et al., 2015) according to the reference genome. Differential gene expression was determined by DESeq2 with the gene count matrix generated by StringTie at the threshold of |log2(Fold Change)|≥1 and adjust P value <0.05.
For ATAC-seq analysis, the filtered reads were mapped to the reference genome using Bowtie2 v 2.2.6 (Langmead and Salzberg, 2012) with parameters “--no-unal --threads 8 --sensitive -k 1 -q”. Redundant reads were removed using Picard v2.60 (http://broadinstitute.github.io/picard/). Peak-calling was using MACS2 (version 2.1.0) (Zhang et al., 2008) with parameters “--nomodel --shift -100 --extsize 200”. If multiple peaks resided within 50 bp to each other, they were considered as a single peak. For differential peak analysis we used DiffBind (Stark & Brown, 2011) based on DESeq2 method. The differential peaks were filtered out by the threshold of log2(Fold Change) ≥0.5, FDR<0.05, and P value <0.05.
Genome_build: RGAP 7
Supplementary_files_format_and_content: For RNA-Seq, each .tab file contains coverage, FPKM, and TPM for the sample. For ATAC-Seq, pooled reads dencity of the three replicates is presented by the bigWig file.
|
| |
|
| Submission date |
Aug 26, 2019 |
| Last update date |
Jun 04, 2020 |
| Contact name |
Yu Chang |
| E-mail(s) |
yuchang@mail.hzau.edu.cn
|
| Organization name |
Huazhong Agricultural University
|
| Department |
National Key Laboratory of Crop Genetic Improvement
|
| Street address |
No.1, Shizishan Street, Hongshan District
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL23876 |
| Series (1) |
| GSE136373 |
A lamin-like protein OsNMCP1 regulates drought resistance and root growth partially through chromatin accessibility modulation by interacting with a chromatin remodeler OsSWI3C in rice |
|
| Relations |
| BioSample |
SAMN12637838 |
| SRA |
SRX6779684 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
