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Status |
Public on Oct 08, 2022 |
Title |
RNA-seq pol2a-1_meiocyte_2 |
Sample type |
SRA |
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Source name |
Meiocyte
|
Organism |
Arabidopsis thaliana |
Characteristics |
tissue: Meiocytes isolated from stage 9-10 floral buds genotype: pol2a-1
|
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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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|
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
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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 |
SAMN28532302 |
SRA |
SRX15331854 |