 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 28, 2019 |
| Title |
CK: spores |
| Sample type |
SRA |
| |
|
| Source name |
spores
|
| Organism |
Penicillium expansum |
| Characteristics |
cell type: spores
treatment: spores in NYDB medium
|
| Treatment protocol |
The sample of Y is treated with Meyerozyma guilliermondii, sample CK was the control group.
|
| Growth protocol |
Penicillium expansum treated with Meyerozyma guilliermondii was inoculated in NYDB medium, an was incubated at 25C, 120 rpm. For 24 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spores were collected, 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 |
Illumina HiSeq 2000 |
| |
|
| 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 |
Feb 27, 2019 |
| Last update date |
Feb 28, 2019 |
| Contact name |
Qiya Yang |
| E-mail(s) |
yangqiya1118@163.com
|
| Phone |
+86-18205041471
|
| Organization name |
Jiangsu University
|
| Street address |
Xuefu ROAD 301
|
| City |
Zhenjiang |
| ZIP/Postal code |
212013 |
| Country |
China |
| |
|
| Platform ID |
GPL26230 |
| Series (1) |
| GSE127259 |
Transcriptome characterization of Penicillium expansum induced by Meyerozyma guilliermondii |
|
| Relations |
| BioSample |
SAMN11029025 |
| SRA |
SRX5441673 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
