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| Status |
Public on May 31, 2021 |
| Title |
plus CdH2 small RNA |
| Sample type |
SRA |
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| Source name |
Leaf
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| Organism |
Populus deltoides |
| Characteristics |
strain: monilifera (Aiton) Eckenw
developmental stage: 89 d
culture: sand culture + hydroponics
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| Treatment protocol |
After treated with 0 (low, L), 100 (middle, M), or 1500 (high, H) µM SO42- for 12 days, the plants were exposed to either 0 (-Cd) or 50 (+Cd) μM CdCl2 together with the S treatments for 21 additional days.
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| Growth protocol |
Stem cuttings of Populus deltoides were rooted and planted in plastic pots and irrigated with 50 mL modified Hoagland nutritional solution in the evening of every other day. After 8 weeks, 72 plants with similar height and growth performance were selected and cultivated in hydroponics using modified Hoagland nutritional solution which was refreshed every 2 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted in the leaves of poplars using Trizol reagent (Invitrogen, CA, USA) following the manufacturer’s procedure with minor modifications. The quantity and purity (RIN number >7.0) of the extracted RNA were analyzed by Bioanalyzer 2100 (Agilent, Santa Clara, CA, USA) and RNA 6000 Nano LabChip Kit (Agilent, CA, USA). Afterwards, the extracted RNA samples were treated with total RNA purification kit (TRK1001, LC Science, Houston, TX) to eliminate genomic DNA contamination.
For mRNA sequencing, the purified total RNA from each sample was reverse-transcribed to create the cDNA library according to the protocol of the RNA-sequencing sample preparation kit (Illumina, San Diego, USA). For small RNA sequencing, the extracted RNA was used to construct a small RNA library using TruSeq Small RNA Prep Kits (RS-200, Illumina, CA, USA). For degradome sequencing, equal amounts of the 9 RNA samples from poplar leaves treated with either 0 or 50 µM CdCl2 were mixed to form a pooled sample. About 150 ng of RNA with poly(A) was annealed and captured with biotinylated random primers. Then, the RNAs containing 5’-monophosphates were ligated to 5’ adaptor and transcribed to cDNAs
Total mRNA sequencing was performed on an Illumina Hiseq2000/2500 sequencer (Illumina, CA, USA).The single-end sequencing was performed on an Illumina Hiseq2500 sequencer (Illumina, CA, USA) at the LC Science (Hangzhou, China) following the vendor’s recommended protocol for small RNA sequenceing and degradome sequencing.
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| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
plus CdH2
small RNA
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| Data processing |
Raw reads were obtained using Illumina’s Pipeline (Version 1.5) following sequencing image analysis and base-calling
Potentially cleaved transcripts were identified by CleaveLand (version 3.0).
The high-quality reads were mapped to the genome sequence of P. trichocarpa using Tophat package (version 2.1.1)
The FPKMs were calculated using a protocol from Pertea et al. Nature Biotechnology, 2015
Genome_build: version 3.0
Supplementary_files_format_and_content: Tab-defined each excel files include FPKMs for each samples
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| Submission date |
Dec 24, 2019 |
| Last update date |
May 31, 2021 |
| Contact name |
Hong Yu Zhang |
| E-mail(s) |
zhangyuhong1112@126.com
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| Organization name |
Chinese Academy of Forestry
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| Department |
Research Institute of Forestry
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| Lab |
State Key Laboratory of Tree Genetics and Breeding
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| Street address |
Qinglongqiao Street
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| City |
Beijing |
| ZIP/Postal code |
100091 |
| Country |
China |
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| Platform ID |
GPL27948 |
| Series (1) |
| GSE142565 |
Physiological and transcriptomic analyses reveal sulfur is essential for cadmium detoxification and accumulation in poplar leaves |
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| Relations |
| BioSample |
SAMN13675869 |
| SRA |
SRX7437696 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4232004_+CdH2-miRNA.xlsx |
329.1 Kb |
(ftp)(http) |
XLSX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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