|
| Status |
Public on Jul 30, 2016 |
| Title |
A1_mRNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
China
|
| Organism |
Gossypium hirsutum |
| Characteristics |
genotype: dwarf mutant Ari1327 (A1)
tissue: stem apexes
developmental stage: At the fifth true leaf stages
|
| 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.
|
| 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.
|
| 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
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
The raw image data was transformed by base-calling into sequence data and stored in fastq format. To control for the influence of error rate in the Solexa data results, quality pretreatment of the raw data was performed: the sliding window method was first used to remove low-quality fragments (quality threshold = 20, error rate = 1%, window size = 5 bp, and length threshold = 35 bp), followed by removal of partial (<35 bp) sequences containing “N” from the reads.
After filtering of low-quality and dirty raw reads, transcriptome de novo assembly was carried out using the paired-end assembly method as implemented in Trinity (http://trinityrnaseq.sourceforge.net/; trinityrnaseq_r2012-10-05) [123]. After removal of repeats from the spliced sequences, transcripts were obtained of the expected length and size.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
|
| |
|
| Submission date |
Jul 31, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Du Xiongming |
| E-mail(s) |
dujeffrey8848@hotmail.com
|
| Organization name |
Institute of cotton research of CAAS
|
| Street address |
38# Huanghe Avenue
|
| City |
Anyang |
| State/province |
Henan |
| ZIP/Postal code |
455000 |
| Country |
China |
| |
|
| Platform ID |
GPL16485 |
| Series (1) |
| GSE71608 |
MicroRNA and mRNA expression profiling analysis revealed the regulation of plant height in Gossypium hirsutum |
|
| Relations |
| BioSample |
SAMN03946305 |
| SRA |
SRX1127458 |
