|
| Status |
Public on Jul 05, 2023 |
| Title |
control 3 |
| Sample type |
SRA |
| |
|
| Source name |
hypocotyls of melon seedlings, submerged ,2day
|
| Organism |
Cucumis melo |
| Characteristics |
tissue: hypocotyls of melon seedlings
cultivar: Xizhoumi No. 25
treatment: control
time: Day 0
|
| Treatment protocol |
control treatment (Control): the hypocotyls of melon seedlings were submerged in water.
SL treatment (GR24): the hypocotyls of melon seedlings were submerged in 0.1 mg/L of GR24.
SL and IAA treatment (GR24+IAA): the hypocotyls of melon seedlings were submerged in 0.1 mg/L of GR24 and 250 mg/L of IAA.
|
| Growth protocol |
Melon seeds of ‘Xizhoumi No. 25’ were placed in culture dishes with wet filter paper and then cultured in an incubator at 28°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
After treatment, the cut hypocotyls of 12 plants in each treatment were placed in liquid nitrogen for RNA-Seq, and 30 plants from each treatment group were cultured in half-strength Murashige and Skoog medium for AR formation.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina HiSeq 4000 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: DHL92 4.0
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Jun 07, 2023 |
| Last update date |
Jul 05, 2023 |
| Contact name |
li jing rui |
| E-mail(s) |
yyljr@hebau.edu.cn
|
| Phone |
13013250913
|
| Organization name |
HeBei Agricultural University
|
| Street address |
lekainan Street
|
| City |
Baoding |
| ZIP/Postal code |
071033 |
| Country |
China |
| |
|
| Platform ID |
GPL33469 |
| Series (1) |
| GSE234393 |
Transcriptome analysis reveals that auxin promotes strigolactone-induced adventitious root growth in the hypocotyl of melon seedlings |
|
| Relations |
| BioSample |
SAMN35668480 |
| SRA |
SRX20635142 |
