|
| Status |
Public on Oct 08, 2019 |
| Title |
WT_mRNA_2 |
| Sample type |
SRA |
| |
|
| Source name |
seedings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
developmental stage: two-week
ecotype: Col-0
genotype: WT
|
| Growth protocol |
Arabidopsis seedlings were grown in a growth chamber (Percival) at 23℃ with 16h light
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from 12-day-old WT and mutant seedlings using TRI reagent (MRC, TR118) according to the manufacturer’s instructions.
RNA-seq libraries were constructed using TruSeq RNA Library Prep Kit v2 (Illumina, RS-122-2001 and RS-122-2002)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Base-caling was performed by the sequncing company, using Illumina Casava.
Raw reads were mapped to the Araport11 genome using STAR v2.6 with the parameters "--alignIntronMax 5000 --outSAMmultNmax 1 --outFilterMultimapNmax 50 --outFilterMismatchNoverLmax 0.1".
Mapped reads were counted by featureCounts v1.6.4.
All above processing procedures were integrated into a homemade pipeline pRNASeqTools (https://github.com/grubbybio/pRNASeqTools)
Genome_build: Araport11
Supplementary_files_format_and_content: Tab-delimited text files containing the gene accession, number of raw read counts, and transcript length.
|
| |
|
| Submission date |
Jun 27, 2019 |
| Last update date |
Oct 08, 2019 |
| 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) |
| GSE133411 |
FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis [RNA-seq] |
| GSE133461 |
FIERY1 promotes microRNA accumulation by suppressing rRNA-derived small interfering RNAs in Arabidopsis |
|
| Relations |
| BioSample |
SAMN12148449 |
| SRA |
SRX6373258 |
