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| Status |
Public on Aug 01, 2018 |
| Title |
cold-acclimated (ca_1) |
| Sample type |
SRA |
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| Source name |
leaf
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| Organism |
Camellia sinensis |
| Characteristics |
tissue: mature leaves
treatment: cold-acclimated
sampling date: 29th December, 2010
cultivar: Longjing 43
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| Treatment protocol |
The natural cold acclimation treatment and samples collection was performed.Two samples, including ones that were non-acclimated (CK, the date for sample collection was 1st December, 2010) and fully acclimated (CA1, the date was 29th December, 2010), were used for libraries preparation and further analyses.
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| Growth protocol |
Tea plants (‘Camellia sinensis (L.) O. Kuntze cv. ‘Longjing 43’) were grown in the Tea Research Institute, Chinese Academy of Agricultural Sciences (TRI, CAAS, N 30°10', E 120°5'), Hangzhou, China, were used in this study.
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| Extracted molecule |
total RNA |
| Extraction protocol |
To construct small RNA libraries, total RNA was extracted using the Trizol (Invitrogen) according to the manufacturer's protocols and RNase –Free DNase I was used to remove genomic DNA contimination.
For each sample, the 18-30 nt small RNAs were ligated with 5' and 3' RNA adapter by T4 RNA ligase (TaKaRa) after they were purified by electrophoretic separation on a 15% TBE-urea denaturing PAGE gel, and at each step purified by urea PAGE gel electrophoretic separation. The RNA was subsequently transcribed to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). Thereafter the cDNA was used as templates for double-stranded cDNA synthesis by PCR amplification using primers that anneal to adapters. The purified DNA was sequenced on a Solexa sequencer (Illumina).
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
miRNA
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| Data processing |
After the sequence tags from Solexa sequencing went through the data cleaning by removing the low quality tags (i.e., tags less than 18 nt and tags whose adaptors were null) and contaminants (adaptors and polyA)
After removing adaptor sequences of the left high-quality small RNA reads with exact matches to the adaptor sequences, reads were mapped to the C. sinenesis unigene dataset using SOAP2.
The sequences were used through BLASTn search of the NCBI Genebank database and Rfam database to remove the rRNAs, tRNAs, snRNAs and snoRNAs.
The unique small RNA sequences left were searched against the miRNase database v19.0 and were considered to be known miRNAs with up to two mismatches.The sequences that didn’t map to any known miRNAs were analyzed for predictions to identify novel miRNAs
The sequences that didn’t map to any known miRNAs were analyzed for predictions to identify novel miRNAs
Supplementary_files_format_and_content: fasta files and text files
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| Submission date |
Dec 02, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Lu Wang |
| E-mail(s) |
wanglu317@tricaas.com
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| Organization name |
Tea Research Institute, Chinese Academy of Agricultural Sciences
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| Street address |
9th, South Meiling Road
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| City |
Hangzhou |
| State/province |
Zhejiang |
| ZIP/Postal code |
310008 |
| Country |
China |
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| Platform ID |
GPL19477 |
| Series (1) |
| GSE63760 |
Identification and Differential Expression of MicroRNAs during Cold Acclimation of the Tea Plant (Camellia sinensis) by Deep Sequencing |
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| Relations |
| BioSample |
SAMN03247595 |
| SRA |
SRX792045 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1556788_ca_1_clean.fa.gz |
52.0 Mb |
(ftp)(http) |
FA |
| GSM1556788_ca_1_match_Rfam.txt.gz |
745.2 Kb |
(ftp)(http) |
TXT |
| GSM1556788_ca_1_match_genome.txt.gz |
4.3 Mb |
(ftp)(http) |
TXT |
| GSM1556788_ca_1_match_mirbase.txt.gz |
94.4 Kb |
(ftp)(http) |
TXT |
| GSM1556788_ca_1_miRNA.fa.gz |
3.5 Kb |
(ftp)(http) |
FA |
| GSM1556788_ca_1_mir-novel.fa.gz |
371 b |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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