|
| Status |
Public on Oct 08, 2022 |
| Title |
RNA-seq suvhsuvh9_sdlg_2 |
| Sample type |
SRA |
| |
|
| Source name |
Seedling
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 20-day-old seedlings
genotype: suvh2suvh9
|
| Growth protocol |
All the plants were grown in a greenhouse at 20°C under long-day cycle (16 h light/8 h dark, humidity 75%).
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
For meiocyte, 1 U/μL Recombinant RNase Inhibitor (Takara, 2313A) was added to the collection buffer. 300-400 meiocyte masses were used to extract ~400-1000 ng RNA for a biological replicate. The RNA was extracted using Trizol (ThermoFisher, 15596026). For seedling, 4-5 plants were ground in liquid nitrogen and the total RNA was also extracted using Trizol.
RNA-seq libraries were constructed with the TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer’s instructions
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
FASTQ reads were analyzed using the plant sequencing analysis pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools).
raw reads were treated using cutadapt v3.4 to remove the adapters
remaining reads were mapped to TAIR10 using STAR v2.7.9a with parameters “--alignIntronMax 5000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1”.
DE genes and TEs (fold change ≥ 2 and P value< 0.01) were identified by the R package DESeq2 v1.30.1 based on the gene expression matrix quantified by featureCounts v2.0.0.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files containing raw read counts on genes and TEs with annotated length
|
| |
|
| Submission date |
May 18, 2022 |
| Last update date |
Oct 10, 2022 |
| Contact name |
Chenjiang You |
| E-mail(s) |
chenjiang.you@ucr.edu, youchenjiang2003@hotmail.com
|
| Organization name |
Fudan University
|
| Street address |
2005 Songhu Rd
|
| City |
Shanghai |
| State/province |
Shanghai |
| ZIP/Postal code |
200438 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (2) |
| GSE203309 |
DNA polymerase epsilon interacts with SUVH2/9 to mediate meiotic DSB associated gene silencing beyond DNA methylation in Arabidopsis [RNA-seq] |
| GSE203328 |
DNA polymerase epsilon interacts with SUVH2/9 to mediate meiotic DSB associated gene silencing beyond DNA methylation in Arabidopsis |
|
| Relations |
| BioSample |
SAMN28532288 |
| SRA |
SRX15331868 |
