|
| Status |
Public on Aug 14, 2019 |
| Title |
Degradation_Col_0h_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Degradation_Col_0h
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
ecotype background: Col
developmental stage: 2-week seedlings
treatment: cordycepin for 0 hour
|
| Treatment protocol |
The seedlings grown at 23°C under 16 h of light followed by 8 h of darkness
|
| Growth protocol |
The wild-type Col, atpabs mutants and AtPABs complementary lines were grown on Murashige and Skoog plates with 3% Suc for 14 days
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The seedlings were ground into a fine power in liquid nitrogen and processed using Trizol reagent (Invitrogen).
CLIP-seq libraries generated from Col and AtPABs complementary lines were constructed following the published method in Arabidopsis (Zhang et al., 2015). Ribosome profiling libraries generated from Col and atpabs were constructed following the published method in Arabidopsis (Juntawong et al., 2014). Strand-specific RNA-Seq libraries generated from Col, atpabs were constructed mRNA-Seq library by SMART method (Levin et al., 2010).PolyA-seq library generated from Col was constructed following treated total RNA with RQ1 DNase and RNase T1, purified poly(A)-containing RNA fragments and ligated with adaptors.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
high-throughput profiling of transcriptome in Col (wild type) treated with cordycepin for 0 hour
C3-0_L5_310X10
|
| Data processing |
CLIP-seq reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using NovoAlign. Pyicoclip was used to identify AtPABs binding clusters.
Ribosome profiling reads were trimed using FASTX toolkit. PCR duplications were excluded. Clean tags were then aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count.
RNA-seq reads were aligned to the Arabidopsis genome (TAIR10) using TopHat2. Read counts of genes were counted using htseq-count. Differentially expressed genes were detected using R package edgeR.
Poly(A) tail reads were trimmed and aligned to the Arabidopsis genome (TAIR10) using Bowtie2.
Genome_build: TAIR10
Supplementary_files_format_and_content: bigWig files were generated using bedGraphToBigWig program
|
| |
|
| Submission date |
Aug 13, 2019 |
| Last update date |
Aug 14, 2019 |
| Contact name |
xiaofeng cao |
| E-mail(s) |
xfcao@genetics.ac.cn
|
| Phone |
86-10-64869203
|
| Organization name |
Institute of Genetics and Developmental Biology
|
| Department |
State Key Laboratory of Plant Genomics
|
| Street address |
West Lincui Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL23157 |
| Series (1) |
| GSE110342 |
Impact of G-content on Arabidopsis AtPAB binding and their role in enhancing translational efficiency |
|
| Relations |
| BioSample |
SAMN12566069 |
| SRA |
SRX6707678 |
