|
| Status |
Public on Dec 31, 2019 |
| Title |
6h |
| Sample type |
SRA |
| |
|
| Source name |
Fungus and apple
|
| Organisms |
Penicillium expansum; Malus pumila |
| Characteristics |
treatment: Penicillium expansum spores inoculate on Malus pumila Mill
time: 6h
growth: 95 % relative humidity, 25 C
|
| Treatment protocol |
The sample of 0h is the control which did not contact before extract RNA, sample 1h was inoculated on apple tissues at 1 hour post inoculation,sample 3h was inoculated on apple tissues at 3 hour post inoculation, sample 6h was inoculated on apple tissues at 6 hour post inoculation.
|
| Growth protocol |
Penicillium expansum spores inoculate on Malus pumila Mill for 0, 1, 3, 6h and cultured at 95% relative humidity, 25℃
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Apple tissues after inoculated Penicillium expansum spores were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. 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.
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample …
|
| |
|
| Submission date |
Aug 24, 2018 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Kaili Wang |
| E-mail(s) |
1007059709@qq.com
|
| Phone |
18851407608
|
| Organization name |
Jiangsu University
|
| Department |
School of food and biological engineering
|
| Street address |
Xuefu Road 301
|
| City |
Zhenjiang |
| State/province |
Jiangsu |
| ZIP/Postal code |
212013 |
| Country |
China |
| |
|
| Platform ID |
GPL25489 |
| Series (1) |
| GSE119039 |
The transcriptome of Penicillium expansum and apple interaction during early infection |
|
| Relations |
| BioSample |
SAMN09910614 |
| SRA |
SRX4609177 |
