|
| Status |
Public on May 26, 2021 |
| Title |
WT_root tips_sRNA-seq_rep3 |
| Sample type |
SRA |
| |
|
| Source name |
Root tips of 5-day old seedlings
|
| Organism |
Arabidopsis thaliana |
| Characteristics |
tissue: root tips
developmental stage: 5 days after germination
genotype: wildtype
|
| Treatment protocol |
The seedlings grown at 21-22°C under a 16 h light and 8 h dark cycle.
|
| Growth protocol |
The wild-type and rh27-2 line were grown on 1/2 Murashige and Skoog plates with 1% sucrose for 5 days after germination.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The shoot apices or root tips were ground into fine powder in liquid nitrogen and processed using miRNeasy Mini Kit (217004, Qiagen).
Both small RNA-sequencing and mRNA-sequencing libraries generated from Col-0 wild-type and rh27-2 samples constructed following standard protocols (Berry Genomics).
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
high-throughput profiling of small RNA in Col-0 (wild type) root tips
|
| Data processing |
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.
Small RNA sequencing reads were aligned to the Arabidopsis genome (TAIR10) using Bowtie2. miRNA were aligned to mature miRNA sequence from miRBase using NCBI blast. miRNAs with RPM fold change over 1.5 were defined as differentially expressed miRNAs.
Genome_build: TAIR10
Supplementary_files_format_and_content: read count files were generated using htseq-count program. miRNA abundance files were generated using miRNA counts normalized against total mapped reads.
|
| |
|
| Submission date |
Jul 15, 2020 |
| Last update date |
May 26, 2021 |
| Contact name |
Jing Sun |
| Organization name |
Chinese Academy of Sciences
|
| Department |
IGDB
|
| Street address |
No. 1 West Beichen Road
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL19580 |
| Series (1) |
| GSE154473 |
DEAD-box RNA helicase 27-Mediated MicroRNA Biogenesis Is Essential for Zygote Division and Stem Cell Homeostasis in Arabidopsis |
|
| Relations |
| BioSample |
SAMN15543032 |
| SRA |
SRX8736716 |
