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| Status |
Public on Feb 09, 2017 |
| Title |
Xa |
| Sample type |
SRA |
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| Source name |
boron-deficiect roots
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| Organism |
Citrus sinensis |
| Characteristics |
cultivar: Xuegan
developmental stage: seedlings
tissue: root apices
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| Treatment protocol |
Xa(B-deficient ,0 μM H3BO3),Xb(B-sufficient ,10 μM H3BO3)
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| Growth protocol |
5-week-old seedlings of ‘Xuegan’ [Citrus sinensis (L.) Osbeck] were transplanted into 6 L pots containing fine river sand. Ten weeks after transplanting, each pot was supplied every other day with B-deficient (0 μM H3BO3) or -sufficient (10 μM H3BO3, control) nutrient solution for 15 weeks. There were 10 replications per B treatment with 2 pots in a completely randomized design.
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| Extracted molecule |
total RNA |
| Extraction protocol |
About 0.1 g mixed frozen B-sufficient and -deficient roots from five replictations were used to extract RNA. Total RNA was extracted from frozen roots using TRIzol reagent (Invitrogen, Carlsbad, CA)
Small RNA samples were sequenced by Beijing Genomics Institute (BGI) (Shenzhen, Guangdong, China) using the high throughput pyrosequencing technology developed by Illumina. Two sRNA libraries were constructed, sRNAs were isolated from the total RNA by size fractionation with 15% Tris-borate-EDTA urea polyacrylamide gel (TBU). Then the sRNAs were ligated with 5' and 3' adaptor by T4 RNA ligase after being dephosphorylatd by alkaline phosphatase. The adaptor-ligated sRNAs were transcribed to single-stranded cDNA using Superscript II reverse transcriptase (Invitrogen). Thereafter, the single-stranded cDNA was used as templates for double-stranded synthesis by PCR amplification using the primer designed according to the adapter sequence. The obtained PCR products were sequenced on a Solexa sequencer (Illumina) at the Beijing Genomics Institute (BGI), Shenzhen, China.
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
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| Description |
5-mm-long Citrus sinensis root apices were excised from the seedlings
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| Data processing |
Basecalls performed
Get rid of some contaminant reads from the fq file and get the final clean reads.
The clear reads were mapped to Citrus clementina genome (JGI version 0.9, http://www.phytozome.org/clementine.php, 35976 sequences) using SOAP, only perfectly mapped sequences were retained and analyzed further. rRNAs, tRNAs, snRNAs and snoRNAs were removed from the sRNAs sequences through BLASTn search using NCBI Genebank database (http://www.ncbi.nlm.nih.gov/blast/Blast.cgi/) and Rfam (10.1) database (http://www.sanger.ac.uk/resources/databases/rfam.html) (e = 0.01). The remaining sequences were aligned with known plant miRNAs from miRBase 18 (http://www.mirbase.org/).
Reads that were not annotated were used to predict novel miRNAs using a prediction software Mireap (http://sourceforge.net/projects/mireap/), which was developed by the BGI
Genome_build: citrus clementina genome v0.9 (JGI)
Supplementary_files_format_and_content: txt files with cleaned reads; At series level, supplementary files include counts associated with specific miRNAs and stastical analysis to identify differentially expressed miRNAs.
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| Submission date |
Apr 23, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Chen Lisong |
| E-mail(s) |
lisongchen@fafu.edu.cn
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| Phone |
+8613599390418
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| Organization name |
Fujian Agriculture and Forestry University
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| Street address |
Shangdian street NO.15
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| City |
Fuzhou |
| ZIP/Postal code |
350002 |
| Country |
China |
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| Platform ID |
GPL9256 |
| Series (1) |
| GSE57016 |
Identification of boron-deficiency-responsive microRNAs in Citrus sinensis roots by Illumina sequencing |
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| Relations |
| BioSample |
SAMN02732371 |
| SRA |
SRX525045 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1372975_Xa_clean.txt.gz |
37.8 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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