|
| Status |
Public on Apr 12, 2019 |
| Title |
dcl3b knockdown mutant rice replicate1 |
| Sample type |
SRA |
| |
|
| Source name |
young panicles before heading date, dcl3b knockdown
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
genotype/variation: dcl3b knockdown mutant
tissue: young panicles
|
| Treatment protocol |
N/A
|
| Growth protocol |
Rice plants were grown in the paddy field.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted using Trizol (Sigma), and then were treated with TURBO DNA-free kit (Ambion) for removing DNA contamination.
Libraries were constructed through applying TruSeq Small RNA sample preparation and TruSeq Stranded mRNA kits (Illumina, San Diego, CA, USA) for small RNA sequencing and RNA sequencing, respectively, in accordance with the manufacturer’s instruction.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
dcl3b rep1
dcl3b-rp1
Oryza Sativa subsp. Japonica
mRNA
Strand-specific RNA-seq
processed data file: dcl3b_upregulated.xls
processed data file: dcl3b_downregulated.xls
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Clean reads were acquired from initial pair-end reads after trimming low quality (Q < 20) and adaptor sequences by SeqPrep version 1.1.
Reads aligned to rice genome by TopHat version 2.1.0 with no more than two mismatches.
Differentially expressed genes were identified with the edgeR package. Classic model of edgeR was used for the differential expression analysis with false discovery rate (FDR) of 0.05 and two-fold change of Fragments Per Kilobase of gene per Million mapped reads (FPKM) as significant cutoffs.
Functional enrichment analysis was performed using GOstats. With the hypergeometric test p-value less than 0.05 as threshold.
Clean reads of siRNA samples aligned to rice genome using Bowtie version 1.1.2 with no mismatches. With FDR less than 0.05 and expression level fold change more than five as threshold, we got the siRNA different expression regions.
Genome_build: Oryza sativa Genome Annotation Project Release 7
Supplementary_files_format_and_content: dcl3b_upregulated.xls, dcl3b_downregulated.xls: Excel files of FPKM values and annotation for DEGs.
Supplementary_files_format_and_content: dcl3b_21nt_siRNA_DER.xls, dcl3b_24nt_siRNA_DER.xls: Excel files include differentially expressed regions generated from the small RNA-seq samples.
|
| |
|
| Submission date |
Aug 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Dong Wang |
| E-mail(s) |
dongwang@ncu.edu.cn
|
| Phone |
(86) 15921240757
|
| Organization name |
Nanchang University
|
| Street address |
Hong Gu Tan New Road, No. 999
|
| City |
Nanchang |
| State/province |
JiangXi |
| ZIP/Postal code |
330031 |
| Country |
China |
| |
|
| Platform ID |
GPL18525 |
| Series (1) |
| GSE102747 |
Down-regulated expression of OsDCL3b affects small RNA biogenesis and panicle development in rice |
|
| Relations |
| BioSample |
SAMN07512875 |
| SRA |
SRX3098665 |
