|
| Status |
Public on Sep 22, 2015 |
| Title |
SLOX_C2_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Fruit
|
| Organism |
Solanum lycopersicum |
| Characteristics |
variety: Ailsa Craig
genotype/variation: transgenic expressing citrus gene CsMYBF1
|
| Treatment protocol |
No treatment
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by Trizol method
20 mg total RNA was prepared to enrich mRNA by using the oligo (dT) magnetic beads. After adding fragmentation buffer, the mRNA was interrupted to short fragments (approximately 200 bp). The first strand cDNA was then synthesized with random hexamer-primer using the mRNA fragments as templates. Buffer, dNTPs, RNase H and DNA polymerase I were added to synthesize the second strand. The double-strand cDNA was purified with QiaQuick PCR extraction kit and washed with EB buffer for end repair and single nucleotide A (adenine) addition. Finally, sequencing adaptors were ligated to the fragments.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
replicate 2 for transgenic samples
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Solanum lycopersicum whole genome using Top Hat.
Assembles the matched reads to estimates their abundances using HTSeq.
Genome_build: Reference genome sequences and annotations were downloaded from the tomato genome websit (http://solgenomics.net/organism/Solanum_lycopersicum/genome)
Supplementary_files_format_and_content: Excel file includes RPKM values for each Sample
|
| |
|
| Submission date |
Sep 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
chaoyang Liu |
| E-mail(s) |
chyliu@webmail.hzau.edu.cn
|
| Phone |
+86-027-87281796
|
| Organization name |
Key Laboratory of Horticultural Plant Biology (Ministry of Education)
|
| Department |
Huazhong Agricultural University
|
| Lab |
er
|
| Street address |
Huazhong Agricultural University, Wuhan, 430070, China.
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL16345 |
| Series (1) |
| GSE73300 |
Expression analysis of CsMYBF1 overexpressing tomato fruit |
|
| Relations |
| BioSample |
SAMN04100283 |
| SRA |
SRX1271565 |
