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| Status |
Public on Jul 30, 2016 |
| Title |
A9_small RNA-seq |
| Sample type |
SRA |
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| Source name |
China
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| Organism |
Gossypium hirsutum |
| Characteristics |
genotype: wild type Ari971 (A9)
tissue: stem apexes
developmental stage: At the fifth true leaf stages
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| Treatment protocol |
At the fifth true leaf stages, stem apexes of wild type and mutant seedlings were harvested and immediately frozen in liquid nitrogen and stored at -80°C until further use.
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| Growth protocol |
The seeds of upland cotton, Ari971, wild type (G. hirsutum cv.) and its dwarf mutant (Ari1327) and tall-culm mutant (Ari3697) were surface sterilized in 30% H2O2 for three hours, washed with distilled water for three times, and then soaked in distilled water for one day at room temperature. Sterilized seeds were grown and maintained in pots in a greenhouse at a day/night temperature of 28/22°C with a 14-h photoperiod.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was purified from stem apexes of three samples (Ari971, Ari1327 and Ari3697) using Trizol reagent (Invitrogen) according to the manufacturer’s protocols. Equal amounts of RNA from Ari971, Ari1327 and Ari3697 were pooled for transcriptome and small RNA libraries construction.
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 |
After removal of low-quality reads and adapter sequences from the Solexa sequencing reads, unique sequences of 17–35 nt were used for further analysis.
First, the unique sequences were queried against ribosomal and transfer RNAs from tRNAdb (http://trna.bioinf.uni-leipzig.de/DataOutput/Search), SILVArRNA (http://www.arb-silva.de/), and NONCODE v3.0 (http://www.noncode.org/NONCODERv3/; plant database only, single-nt mismatches allowed) databases to obtain matching rRNA, tRNA, snRNA, and snoRNA sequences.
Any small RNA sequences having exact matches to these sequences were removed from the analysis. The remaining unique small RNA sequences were then BLASTn-searched against the conserved plant miRNAs in the miRBase database (miRBase 19.0; www.mirbase.org/) to identify conserved miRNAs. Only perfectly matched sequences were considered to be conserved miRNAs.
miRNA expression abundance in each library was calculated as RPM (reads per million) according to the formula RPM = mapped reads × 106 / total reads. Calculation of P-values for comparing the miRNA expression between salt-treated samples and the control sample was based on previously established methods(Audic S et al.,1997)
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| Submission date |
Jul 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Du Xiongming |
| E-mail(s) |
[email protected]
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| Organization name |
Institute of cotton research of CAAS
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| Street address |
38# Huanghe Avenue
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| City |
Anyang |
| State/province |
Henan |
| ZIP/Postal code |
455000 |
| Country |
China |
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| Platform ID |
GPL16485 |
| Series (1) |
| GSE71608 |
MicroRNA and mRNA expression profiling analysis revealed the regulation of plant height in Gossypium hirsutum |
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| Relations |
| BioSample |
SAMN03946310 |
| SRA |
SRX1127463 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1841183_A9_clean_miRNA.fa.gz |
3.5 Mb |
(ftp)(http) |
FA |
| GSM1841183_A9_miRNA_rpm.txt.gz |
2.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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