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| Status |
Public on Feb 09, 2017 |
| Title |
S-CK |
| Sample type |
SRA |
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| Source name |
shoot
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| Organism |
Salicornia europaea |
| Characteristics |
tissue: shoot
treatment: control plants
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| Treatment protocol |
control plants
The 30-days old S. europaea seedlings were salinized with 200 mM NaCl for 12 h and 7 d. The plants without NaCl treatment was used as control. To make sure all materials collected having the same biological age and growth rhythm, they were treated separately with NaCl at different time points while harvested at the same time.
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| Growth protocol |
The seeds of S. europaea were sown on vermiculite damped with tap water. After germination, the seedlings were grown in a greenhouse in Beijing Botanical Garden maintained at a thermo period of 25 °C /20 °C day/night temperature, photoperiod of 16 h, and a relative humidity of 50 ± 10%. The seedlings were irrigated weekly with half-strength Hoagland nutrient solution for 30 days.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Plant tissues were ground in liquid nitrogen and were added into two volume of extraction buffer containing 2 M NaCl, 25 mM EDTA, 200 mM Tris (pH 8.0), 20 mM sodium borate, 2% PVPP (w/v), 2% CTAB (w/v), 1% LSS (w/v), and 2% b-mercaptoethanol (v/v). The homogenate was then transferred into a sterile disposable polypropylene tube, vortexed vigorously, and incubated at 65°C in a water-bath shaker over 10 min with occasional shaking. Added one volume of chloroform/isoamyl alcohol (24:1, v/v) into the mixture, and then vortexed, followed by centrifuging at 15,000g for 15 min at 4°C. The resulting upper aqueous phase was transferred into another tube containing one volume of water-saturated phenol/chloroform/ isoamyl alcohol (25:24:1, v/v, pH 4.5). Following vortexing, the sample was then centrifuged at 12,000g for 10 min at 4°C. The above step was repeated until a clean interface was observed. The upper phase containing RNA extract was extracted with one volume of chloroform/isoamyl alcohol (24:1, v/v) and centrifuged at 12,000g for 10 min at 4°C. After the upper phase was transferred into another centrifuge tube, a volume of isopropyl alcohol was added into the tube. The mixture was incubated at-20 °C for at least 1 h or sometimes overnight, followed by centrifugation at 15,000g for 15 min at 4°C. Decant the supernatant immediately. The pellet was rinsed with 75% ethanol and collected by centrifugation at 12,000g for 5 min at 4°C for three times. The air-dried pellet was finally dissolved in DEPC-treated water and stored at -80°C.
RNA libraries were prepared for sequencing using standard Illumina protocols
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| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Filtering out artifact sequences using BGI sRNA analysis pipeline.
Genome_build: S. europaea mRNA transcriptome database (NCBI SRA database with accession NO. SRX302090).
Supplementary_files_format_and_content: fasta files including sequence ID, sequence read count and sequence
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| Submission date |
Oct 20, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yinxin Li |
| E-mail(s) |
yxli@ibcas.ac.cn
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| Organization name |
Institute of Botany
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| Department |
Chinese Academy of Sciences
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| Street address |
Nanxincun No. 20, Xiangshan, Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100093 |
| Country |
China |
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| Platform ID |
GPL19315 |
| Series (1) |
| GSE62521 |
High-throughput deep sequencing reveals that microRNAs play important roles in salt adaptation of euhalophyte Salicornia europaea |
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| Relations |
| BioSample |
SAMN03120872 |
| SRA |
SRX736489 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1528214_S-CK_clean.fa.gz |
58.7 Mb |
(ftp)(http) |
FA |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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