|
| Status |
Public on Apr 11, 2012 |
| Title |
cold treatment mRNA degradome seq |
| Sample type |
SRA |
| |
|
| Source name |
spike tissue
|
| Organism |
Triticum aestivum |
| Characteristics |
tissue: spikes
developmental stage: anthers of 1.5 to 3.0 mm in length
treatment: Cold treatment
strain: thermosensitive genic male sterile (TGMS) line
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
We analyzed spikes from anthers at three developmental stages (including the T0 stage): 1.5-mm anthers in which secondary sporogenous cells were formed; 2.2-mm anthers in which all cell layers were present and mitosis had ceased; and 3.0-mm anthers at the meiotic division stage. To maximize the morphological synchronicity of samples at each individual stage, approximately 20 spikes were collected from primary stems at each stage. The spikes at corresponding stages were also harvested from stems of plants kept in control conditions, using leaf age index and anther length as guide. Total RNAs were isolated from spike tissues using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. After total RNA isolation, RNAs from cold-treated and control spike tissues were mixed, respectively. mRNA degradome libraries were constructed following the instructions of the manufacturer.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
RACE |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by BGI mRNA degradome analysis pipeline
Genome_build: Triticum aestivum: UniGene Build #59
Supplementary_files_format_and_content: tab-delimited text files include mRNA tag length, mRNA tag frequency and mRNA tag sequence
|
| |
|
| Submission date |
Apr 10, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhonghui Tang |
| E-mail(s) |
zhonghui.tang@gmail.com
|
| Organization name |
Huazhong Agricultural University
|
| Street address |
Huazhong Agricultural University
|
| City |
Wuhan |
| ZIP/Postal code |
430070 |
| Country |
China |
| |
|
| Platform ID |
GPL10467 |
| Series (1) |
| GSE37134 |
Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing (Degradome-Seq) |
|
| Relations |
| SRA |
SRX139799 |
| BioSample |
SAMN00854597 |
