|
| Status |
Public on Jul 23, 2024 |
| Title |
Mock_nrpd1-3_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
2-week-old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: 2-week-old seedlings
ecotype: Col-0
genotype: nrpd1-3
treatment: Mock
|
| Treatment protocol |
Mock
|
| Growth protocol |
All plants were grown under long photoperiod conditions (16 h light, 22 °C/8 h dark, 18 °C). Two-week-old seedlings were collected for mRNA-seq.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNAs were purified from 2-week-old Arabidopsis seedlings using the RNeasy Plant Mini Kit (QIAGEN, 74904). Poly(A)+ RNAs were isolated using the Dynabeads mRNA Purification Kit (Invitrogen, 61006) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using the NEXTflex RNA-Seq Kit (Bioo Scientific, 5129-01) according to the manufacturer’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Mock_nrpd1-3_rep2
|
| Data processing |
PCR duplicates were removed using unique molecular identifier (UMI) information, and adapters were trimmed using fastp (v0.23.2).
Clean reads were mapped to the reference genome (TAIR10) using HISAT2 (v2.2.1) with default parameters.
The expression level of each gene was normalized to Fragments Per Kilobase of transcript per Million mapped reads (FPKM) using StringTie (v2.1.7) with strand-specific parameter (--rf).
Assembly: Arabidopsis TAIR10
|
| |
|
| Submission date |
Apr 17, 2023 |
| Last update date |
Jul 23, 2024 |
| Contact name |
Yijun Qi |
| E-mail(s) |
qiyijun@mail.tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Department |
School of Life Sciences
|
| Street address |
NO.1 Qinghuayuan
|
| City |
Beiing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL26208 |
| Series (1) |
| GSE229881 |
An RdDM-independent function of Pol V transcripts in gene regulation and plant defense |
|
| Relations |
| BioSample |
SAMN34224085 |
| SRA |
SRX19994270 |
