|
| Status |
Public on Dec 29, 2018 |
| Title |
Vfo_S1 |
| Sample type |
SRA |
| |
|
| Source name |
endosperm
|
| Organism |
Vernicia fordii |
| Characteristics |
developmental stage: 90 days after pollination
tissue: seeds from female flowers pollinated to mature seeds
oil accumulation stage: S1; early/initial stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using CTAB method and treated with RQ1 DNase (promega) to remove DNA.
For each sample, 10 μg of total RNA was used for RNA-seq library preparation. Polyadenylated mRNAs were purified and concentrated with oligo (dT)- conjugated magnetic beads (Invitrogen) before used for directional RNA-seq library preparation. Purified mRNAs were iron fragmented at 95°C followed by end repair and 5' adaptor ligation. The reverse transcription was performed with RT primer harboring 3' adaptor sequence and randomized hexamer. The cDNAs were purified and amplified, and PCR products corresponding to 200-500 bps were purified, quantified and stored at -80 °C until used for sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file: youtong_exp_RPKM.txt
|
| Data processing |
Illumina Casava1.9 software used for basecalling.
3' adapter (GATCGGAAGAGC) trimmed with fastx_clipper
Clean reads assembly by trinity with default parameters
mapped using bowtie -k 2 -v 2
detecting different expression gene using edgeR
Genome_build: youtongshu.fasta for Vfo_S1 and Vfo_S2
Genome_build: mafengshu.fasta for Jcu_S1 and Jcu_S2
Supplementary_files_format_and_content: fasta file for genome, and tab-delimited text files include gene RPKM values for each Sample
|
| |
|
| Submission date |
Dec 29, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Dangquan Zhang |
| E-mail(s) |
[email protected]
|
| Organization name |
Central South University of Forestry and Technology
|
| Street address |
South Shaoshan Road
|
| City |
Changsha |
| ZIP/Postal code |
410004 |
| Country |
China |
| |
|
| Platform ID |
GPL17722 |
| Series (1) |
| GSE76386 |
Differential lipid synthesis in the developing seeds of Jatropha and Vernicia: a comparative transcriptomic study |
|
| Relations |
| BioSample |
SAMN04376179 |
| SRA |
SRX1506726 |
