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| Status |
Public on Apr 10, 2019 |
| Title |
sRNA-seq-T3 |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Camellia sinensis |
| Characteristics |
strain: Shuchazao
treatment: gloeosporioides-inoculated
developmental stage: mature leaf
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| Treatment protocol |
The pathogenic C. gloeosporioides was originally isolated from diseased leaves of Shuchazao at the field of Anhui Agricultural University, Hefei, China. C. gloeosporioides was cultured on potato dextrose agar and incubated at 25 °C ± 2 °C in darkness for 10 days to promote sporulation. Conidia were harvested and suspended in sterile water. The conidia concentration was determined using a hemocytometer and adjusted to 1×10^5 mL-1 for inoculation.
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| Growth protocol |
Three-year-old cuttings were planted in pots (30-cm diameter, 35-cm height) and grown in a green house maintained at 23 ± 3 °C with 65 ± 5% room humidity and a 16/8 h (day/light) photoperiod. All experimental plants were irrigated once a day and fertilized once a month. Healthy Shuchazao cuttings with uniform growth (25−30 cm in height) were selected for experiments.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from each frozen sample using Trizol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. The quantity and quality of the total RNA were determined using a Bioanalyzer 2100 (Agilent, CA, USA) and the RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0.
Equal quantities of total RNA from C. gloeosporioides- and mock-inoculated leaves collected at four days post infection (4dpi) were used to prepare the sRNA libraries using the TruSeq Small RNA Sample Prep Kit (Illumina, San Diego, CA, USA). We performed single-end sequencing (36 bp) on an Illumina Hiseq 2500 at the LC-BIO (Hangzhou, China) using the vendor’s recommended protocol.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer IIx |
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| Description |
All_miRNA_sequence_expression.txt
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| Data processing |
The raw reads of sRNA-seq was generated from the Illumina GAIIX system and the degradome sequencing was sequenced on Illumina Hiseq2500
In sRNA-seq, the raw reads were filtered using the Illumina pipeline filter (Solexa 0.3), and then further processed with the in-house program (ACGT101-v4.2-miR, LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences ranging from 18 to 26 nt in length were compared with known plant miRNAs in miRBase (Release 22; http://www.mirbase.org), using BLAST searches to identify known miRNAs with no more than two mismatches. After the analyses, known miRNAs were categorized into four groups (1a, 1b, 2a, and 3a).
In degradome sequencing ,raw sequencing reads were obtained using Illumina’s Pipeline v1.5 software and processed to remove adaptor sequences and low-quality sequencing reads. The unique sequencing reads with lengths of 20 nt and 21 nt were then used to identify potentially cleaved targets with a public software package (CleaveLand3.0 pipeline)
Genome_build: Camellia sinensis var. sinensis (Sequence Read Archive database accession No. SRA536878, http://pcsb.ahau.edu.cn:8080/CSS/)
Supplementary_files_format_and_content: precursors and mature miRNA sequences,tab-delimited text files include RPKM values for each Sample
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| Submission date |
Sep 10, 2018 |
| Last update date |
Apr 10, 2019 |
| Contact name |
chaoling Wei |
| E-mail(s) |
[email protected]
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| Phone |
008655165786765
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| Organization name |
Anhui Agricultural University
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| Street address |
130 West Changjiang Road
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| City |
Hefei |
| State/province |
Anhui |
| ZIP/Postal code |
230036 |
| Country |
China |
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| Platform ID |
GPL20107 |
| Series (1) |
| GSE119728 |
Identification of regulatory networks of microRNAs and their targets in immunity to Colletotrichum gloeosporioides in tea plant (Camellia sinensis L.) |
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| Relations |
| BioSample |
SAMN10026054 |
| SRA |
SRX4665664 |
| 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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