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| Status |
Public on Aug 01, 2016 |
| Title |
CSV |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Cucumis sativus |
| Characteristics |
tissue: leaf
age: four weeks
protocol: anti-infection cucumber
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| Extracted molecule |
total RNA |
| Extraction protocol |
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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| 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: cucumber ChineseLong v2
Genome_build: ftp://www.icugi.org/pub/genome/cucumber/
Genome_build: Botryotinia fuckeliana B05.10 v2.23
Genome_build: ftp://ftp.ensemblgenomes.org/pub/release-23/fungi/fasta/botryotinia_fuckeliana/dna
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample; For gene ids, please see "cucumber_Chineselong_v2.gff3" in ftp://www.icugi.org/pub/genome/cucumber/
Supplementary_files_format_and_content: CSV and HBC are pure cultured sample. HGBC contain both cucumber and Botrytis cinerea RNA
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| Submission date |
Aug 19, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
kong weiwen |
| E-mail(s) |
kongweiwen90@126.com
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| Organization name |
Beijing forestry university
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| Street address |
Qinghua East Rd 35
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| City |
beijing |
| ZIP/Postal code |
100083 |
| Country |
China |
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| Platform ID |
GPL20825 |
| Series (1) |
| GSE72191 |
Next Generation Sequencing Facilitates Quantitative Analysis of Cucumber and Botrytis cinerea Transcriptome Changes During Infection |
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| Relations |
| BioSample |
SAMN04001491 |
| SRA |
SRX1158863 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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