|
| Status |
Public on Feb 13, 2017 |
| Title |
S04 |
| Sample type |
SRA |
| |
|
| Source name |
Control leaves
|
| Organism |
Citrus sinensis |
| Characteristics |
tissue: matured leaf from 1/3 height of the plants
time point: 15 weeks post B treatment
treatment: 10 μM H3BO3, control
|
| Treatment protocol |
Ten weeks after transplanting, each pot was supplied every other day with B-sufficient (10 μM H3BO3, control) or -toxic (400 μM H3BO3) nutrient solution for 15 weeks. There were 20 replications per B treatment with 2 pots in a completely randomized design.
|
| Growth protocol |
5-week-old seedlings of ‘Xuegan’ (Citrus sinensis) and sour pummelo (C. grandis) were transplanted into 6 L pots containing fine river sand. Seedlings were planted in greehouse under natural light condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf total RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
miRNA_expression.list
|
| Data processing |
The clean reads were mapped to Citrus clementina genome (JGI version 1.0, http://www.phytozome.org/clementine.php) 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 21 (http://www.mirbase.org/).
|
| |
|
| Submission date |
Oct 28, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Chen Lisong |
| E-mail(s) |
lisongchen@fafu.edu.cn
|
| Phone |
+8613599390418
|
| Organization name |
Fujian Agriculture and Forestry University
|
| Street address |
Shangdian street NO.15
|
| City |
Fuzhou |
| ZIP/Postal code |
350002 |
| Country |
China |
| |
|
| Platform ID |
GPL21082 |
| Series (1) |
| GSE74434 |
Illumina miRNA profiles with anatomical study revealed involvement of miR397a in Citrus adaptation to long-term B-toxicity via modulating secondary cell wall biosynthesis |
|
| Relations |
| BioSample |
SAMN04221424 |
| SRA |
SRX1393867 |
