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| Status |
Public on Oct 10, 2014 |
| Title |
hybrid of WVa700 and Micro-Tom |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Solanum lycopersicum x Solanum pimpinellifolium |
| Characteristics |
sample group: hybrid
cultivar: hybrid of WVa700 and Micro-Tom
tissue: leaf
molecule subtype: small RNA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs of young leaves of Micro-Tom, WVa700, Micro-Tom×WVa700 and WVa700×Micro-Tom were extracted using the Trizol reagent (Invitrogen Inc.) according to the manufacturer’s protocol.
The RNAs were sent to the Beijing Genomics Institute (BGI) for sequencing. Small RNAs were enriched and ligated to a 5’ adaptor and a 3’ adaptor sequentially, then converted to cDNA by RT-PCR, and used for Hiseq high-throuput sequencing directly.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
The very basic figure from sequencing is converted into sequence data by the base calling step and such sequence data called raw data or raw reads is stored in the *.fq file. Then, we get rid of some contaminant reads from the fq file through the software developed by BGI to deal with the data from HiSeq sequencing and get the final clean reads for the following analysis. And, contaminant reads contain low quality reads, reads with 5' primer contaminants, reads without 3' primer, reads without the insert tag, reads with poly A and reads shorter than 18nt.
Supplementary_files_format_and_content: fasta files in the format of read_id, count followed by read
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| Submission date |
Oct 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Junxing Li |
| E-mail(s) |
0013956@zju.edu.cn
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| Phone |
08618768141197
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| Organization name |
Institute of Vegetable Science, Zhejiang University
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| Street address |
Yuhangtang Road 866
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| City |
Hangzhou |
| ZIP/Postal code |
310058 |
| Country |
China |
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| Platform ID |
GPL19278 |
| Series (1) |
| GSE62196 |
The role of small RNAs on phenotypes in reciprocal hybrids between Solanum lycopersicum and S. pimpinellifolium |
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| Relations |
| BioSample |
SAMN03100507 |
| SRA |
SRX730563 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1521879_WVa700_Micro-Tom_clean.fa.gz |
36.3 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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