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| Status |
Public on Jun 12, 2017 |
| Title |
Sample_MT_2 |
| Sample type |
SRA |
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| Source name |
Citrus
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| Organism |
Citrus trifoliata |
| Characteristics |
tissue: The terminal bud and the five following buds (the major node position for flower formation) from spring flushes
development stage: After self-pruning
cultivar: Precocious trifoliate orange
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| Treatment protocol |
No treatment
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| Growth protocol |
The terminal bud and the five following buds (the major node position for flower formation) from spring flushes of the MT and the WT 2-year-old trees were also collected at flower initiation (after self-pruning).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from the WT and the MT (three biological replicates per genotype) using the Plant RNAiso Plus according to the manufacturer’s instructions (Takara, Kusatsu, Japan). Genomic DNA was removed from total RNA by DNase treatment (Promega, Madison, WI, USA). All RNA samples were quantified and examined for protein contamination and reagent contamination by a Nanodrop ND 1000 spectrophotometer (NanoDrop, Wilmington, DE, USA). Due to some lncRNAs lacking the poly(A) tail, total RNA was treated to remove rRNA by using Ribo-Zero rRNA Removal Kits (Plant) according to the manufacturer’s instructions (illumina, USA), retaining lncRNA both with and without a poly(A) tail.
Six strand-specific RNA libraries with an insert size of about 250–500 nucleotides were prepared according to a UTP method (Parkhomchuk et al., 2009), and submitted to the Beijing Genomics Institute (BGI, Shenzhen, China) for 125 bp paired-end sequencing on the Illumina HiSeq 2500, at a depth of approximately 90 million reads per library.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
MT_2
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| Data processing |
The original image data is transfered into sequence data by base calling, which is defined as raw data or raw reads and saved as fastq files.
To get the clean reads, removing the dirty raw reads is needed before data analysis. Filter steps: Remove reads with adaptors; Remove reads in which unknown bases are more than 10%; Remove low quality reads (the percentage of the low quality bases of quality value ≤ 5 is more than 50% in a read) .
Clean reads were mapped to reference sequences using SOAPaligner/soap2. Mismatches no more than 2 bases were allowed in the alignment.
The gene expression level is calculated by using RPKM method (Reads Per kb per Million reads).
Denove
Genome_build: No
Supplementary_files_format_and_content: xls files were generated by Microsoft Excel, RPKM represent the expression of genes.
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| Submission date |
Jul 15, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
jin zhi zhang |
| E-mail(s) |
jinzhi327320094@126.com
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| Phone |
86-27-87281899
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| Organization name |
Huazhong Agricultural University
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| Department |
College of Horticulture and Forestry Science
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| Street address |
College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
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| City |
WuHan |
| ZIP/Postal code |
430070 |
| Country |
China |
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| Platform ID |
GPL22161 |
| Series (1) |
| GSE84443 |
Genome-wide screening and characterization of long non-coding RNAs involved in flowering development of citrus (Poncirus trifoliata L. Raf.) by RNA sequencing |
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| Relations |
| BioSample |
SAMN05392705 |
| SRA |
SRX1950774 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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