|
| Status |
Public on Sep 01, 2023 |
| Title |
Z_Y3_3 |
| Sample type |
SRA |
| |
|
| Source name |
seeds
|
| Organism |
Solanum lycopersicum |
| Characteristics |
tissue: seeds
genotype: SlLBD40 knockout
treatment: imbibition
time: 6 hours
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
fastx_toolkit_0.0.14/SeqPrep/Sickle were used for estimating sequencing quality to gain clean reads.
TopHat2/ HISAT2 were used to analysis the mapped data quality.
The mapped reads were spliced using StringTie or Cufflinks software
FPKM Fragmen(ts Per Kilobases per Millionreads) values were used to show gene expression level.
Assembly: SL 3.0; https://solgenomics.net/organism/Solanum_lycopersicum/genome
Supplementary files format and content: text files include FPKM values for each Sample
|
| |
|
| Submission date |
May 13, 2023 |
| Last update date |
Sep 01, 2023 |
| Contact name |
Jialong Zhang |
| E-mail(s) |
bs20223170941@cau.edu.cn
|
| Phone |
18611181786
|
| Organization name |
China Agricultural University
|
| Street address |
Malianwa Street
|
| City |
Beijing |
| ZIP/Postal code |
100094 |
| Country |
China |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE232485 |
Transcriptome analysis of wild type, slbd40 and slwrky37 tomato seeds after imbibition. |
|
| Relations |
| BioSample |
SAMN35069163 |
| SRA |
SRX20326340 |
