|
| Status |
Public on Jan 02, 2023 |
| Title |
TP309_seedling_mRNA_replicate2 |
| Sample type |
SRA |
| |
|
| Source name |
seedling
|
| Organism |
Oryza sativa Japonica Group |
| Characteristics |
tissue: seedling
cultivar: Taipei309
genotype: wildtype
|
| Growth protocol |
Rice plants grown in soil in Jiangsu province
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extrated using TRIzol method.
1.Total RNA used DNaseI to digest DNA, and enriched mRNA using magnetic beads with Oligo(dT). 2.Adding reagent in Thermomixer to interrupt mRNA into short fragments. 3.The fragmented mRNA was used as template to synthesize the first strand of cDNA, and then synthesized the second strand. 4.Purified by using the kit, and repaired the adhesive termination, added the base "A" and adapter in the CDNA 3'end, then selected 200-300bp fragments and performed PCR amplification. 5.The libraries were checked with Agilent 2100 Bioanalyzer and ABI Real-Time PCR System, the qualified libraries were sequenced using sequencing platform.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Description |
TP309_seedling_rep2 mRNA-seq
|
| Data processing |
Low-quality reads had been eliminated.
All reads were mapped onto the O.sativa genome (MSU version 7.0) by Tophat.
Expression level were normalized through fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: MSU version 7.0
|
| |
|
| Submission date |
Jul 15, 2020 |
| Last update date |
Jan 02, 2023 |
| Contact name |
Lili Wang |
| E-mail(s) |
2014201023@njau.edu.cn
|
| Organization name |
Nanjing Agricultural University
|
| Street address |
Weigang No.1
|
| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
| |
|
| Platform ID |
GPL23876 |
| Series (2) |
| GSE154499 |
The Rise and Fall of Billionaire siRNAs during Reproductive Development in Rice |
| GSE154501 |
The Rise and Fall of Billionaire siRNAs during Reproductive Development in Rice |
|
| Relations |
| BioSample |
SAMN15544662 |
| SRA |
SRX8738402 |
