 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 01, 2024 |
| Title |
Jiashi melon Infection by Alternaria alternata 0d, replicate 3 |
| Sample type |
SRA |
| |
|
| Source name |
melon fruit(pulp)
|
| Organism |
Cucumis melo |
| Characteristics |
treatment: Infection by Alternaria alternata
|
| Extracted molecule |
total RNA |
| Extraction protocol |
In total, approximately 1 μg total RNA was initially used for BGISEQ-500 library construction. In general, DNase I was initially used to degrade double-stranded and single-stranded DNA contaminant in RNA samples. The mRNA molecules were then purified from total RNA using oligo(dT)-attached magnetic beads and fragmented into small pieces. First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. The cDNA thus synthesized was subjected to end-repair and 3′ adenylation. Subsequently, adaptors were ligated to the ends of these 3′ adenylated cDNA fragments. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The single stranded circular DNAs were formatted as the final library for Agilent Technologies 2100 bioanalyzer validation and subsequent SE50 sequencing.
RNA libraries were prepared for sequencing using BGISEQ-500 platform
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
BGISEQ-500 |
| |
|
| Description |
fpkm.txt
JA00P_3
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to Cucumis_melo_L_CM3_6_1_MeloV4 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 (FPKM) 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.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Cucumis_melo_L_CM3_6_1_MeloV4
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Mar 03, 2023 |
| Last update date |
Mar 01, 2024 |
| Contact name |
Bai Yu jia |
| E-mail(s) |
saintbyj@126.com
|
| Organization name |
Xinjiang Agricultural University, College of Food Science and Pharmacy
|
| Street address |
Nong Da Dong Lu No. 311, Urumqi, Xinjiang，China
|
| City |
Urumqi |
| ZIP/Postal code |
830052 |
| Country |
China |
| |
|
| Platform ID |
GPL33211 |
| Series (1) |
| GSE226614 |
Transcriptome sequencing of postharvest melon fruit infected by Alternaria alternata |
|
| Relations |
| BioSample |
SAMN33579686 |
| SRA |
SRX19560049 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
