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| Status |
Public on Mar 03, 2015 |
| Title |
4-target |
| Sample type |
SRA |
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| Source name |
tomato leaves
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| Organism |
Solanum habrochaites |
| Characteristics |
development: five-leaf stage
tissue: leaves
treatment: 1, 4, 8, 12, 24 and 48 h after chilling treatment(4°C/4°C)
cultivar: S. habrochaites.cv. LA1777
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| Treatment protocol |
The seedlings were divided into two groups for treatment; one group was exposed to 4°C/4°C for chilling treatment, while the other group was not treated with chilling stress(25°C/20°C).The third leaf from the stem apex was harvested at 1, 4, 8, 12, 24 and 48 h after treatment.
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| Growth protocol |
Seedlings of ‘LA1777’ (S. habrochaites) at the five-leaf stage were used.
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| Extracted molecule |
total RNA |
| Extraction protocol |
To construct two small RNA libraries, samples from the two treatments harvested at different time points were individually subjected to small RNA extraction using an Illumina Truseq Small RNA Preparation kit (LC Sciences, Hangzhou, China). Equal quantities of small RNA extracted from different time points in one treatment group were pooled as one small RNA library, and the two small RNA libraries were then constructed. Following isolation and ligation, the small RNAs were reverse transcribed to cDNA. The purified cDNAs from the two RNA libraries were used for cluster generation on Illumina’s Cluster Station and then sequenced on Illumina GAIIx following vendor’s instruction for running the instrument. A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis. Two degradome libraries were constructed following with methods previously described by German et al.(2008).CleaveLand3.0 and LC Science’s ACGT301-DGEv1.0 program were used to detect potentially sliced targets of conserved and novel miRNA.
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
degradome
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| Data processing |
A proprietary pipeline script, ACGT101-miR v4.2 (LC Sciences), was used for sequencing data analysis (Li et al. 2010; Wei et al. 2011). A Public software package, CleaveLand3.0 was used for analyzing Degradome sequencing data.
Genome_build: SOL Genomics Network (SGN)
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| Submission date |
May 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
xue cao |
| E-mail(s) |
caoxue1109@126.com
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| Organization name |
Nanjing Agricultural University
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| Street address |
Xuanwu District No. 1
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| City |
Nanjing |
| ZIP/Postal code |
210095 |
| Country |
China |
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| Platform ID |
GPL18655 |
| Series (1) |
| GSE57335 |
Identification of chilling stress-responsive tomato microRNAs and their target genes by high-throughput sequencing and degradome analysis |
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| Relations |
| BioSample |
SAMN02746193 |
| SRA |
SRX533640 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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