 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Feb 13, 2017 |
| Title |
4d |
| Sample type |
SRA |
| |
|
| Source name |
fruit
|
| Organism |
Litchi chinensis |
| Characteristics |
Stage: 4d at ambient storage
tissue: pericarp
molecule subtype: small RNA
|
| Treatment protocol |
Two groups of litchi fruit were harvested. One group of fruit was stored at ambient temperature (25°C) for 0d and 4d. The other group was stored at cold temperature (1°C) for 2 weeks before transferred to 25°C, and then kept at 25°C for 1d and 2d.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Pericarp tissues were immediately frozen, crushed in liquid nitrogen. Total RNA was isolated using a previously described method (Yang et al., Journal of Experimental Botany, 2013).
Small RNA libraries and a mixed degradome library were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
sRNA raw reads were preprocessed using Illumina Genome Analyzer Pipeline. After that, all the clean reads were mapped to miRBase 20 (http://www.mirbase.org/), allowing up to two mismatches, to identify known miRNAs in litchi.
MiRCat was applied to fold flanking genome sequence of the unique small RNAs, followed by secondary structure prediction using RNAfold, to identify novel litchi miRNAs. Further criteria for annotation of plant miRNAs according to Meyers et al. (2008) were used to screen for candidate miRNAs.
degradome sequencing reads were analyzed via CleaveLand 3.0 pipeline to detect potentially cleaved miRNA targets.
all the identified targets were annotated by BlastX (E-value<0.00001) to NR and KEGG, followed by GO term analysis.
Genome_build: litchi unigene assembly (submitted & in review)
Supplementary_files_format_and_content: spreasheets include sequncing statistic, known & novel miRNA lists, miRNA target list etc.
|
| |
|
| Submission date |
Nov 26, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
HONG ZHU |
| E-mail(s) |
zhuhong@scbg.ac.cn
|
| Phone |
86-15920390530
|
| Organization name |
SOUTH CHINA BOTANICAL GARDEN,CHINESE ACADEMY OF SCIENCES
|
| Street address |
723 XINGKE RD.TIANHE DISDRICT
|
| City |
GUANGZHOU |
| State/province |
GUANGDONG |
| ZIP/Postal code |
510650 |
| Country |
China |
| |
|
| Platform ID |
GPL19467 |
| Series (1) |
| GSE63658 |
MicroRNAs and targets in senescent fruit of litchi during ambient storage and post cold storage shelf-life. |
|
| Relations |
| BioSample |
SAMN03222773 |
| SRA |
SRX768729 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
