|
| Status |
Public on Jul 01, 2017 |
| Title |
Yuyu 22 |
| Sample type |
SRA |
| |
|
| Source name |
embryo from the seeds
|
| Organism |
Zea mays |
| Characteristics |
cultivar: Yuyu 22
tissue: whole embryo
treatment: 24 hours soaked seeds at 26°C
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from the all samples was extracted with TRIzol reagent (Invitrogen, 15596-026) following the manufacturer’s protocol.
Small RNA libraies were constructed by TruSeq Small RNA Sample Prep Kit (Illumina) following the manufacturer’s instructions. Briefly, 1 µg total RNA or purified small RNA was ligated with 3’ and 5’ adaptors and used as a template for RT-PCR. After PCR amplification, 6 µL of each sample were pooled and separated on a 6% polyacrylamide Gel. Gel slices corresponding to ~18-26 nt small RNAs were recovered.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Base-call using Illumina's RTA package.
Quality access by FastQC.
Adapter sequences were trimmed by fastx.
Summary fastq to reads and counts by Perl script.
sRNAs were aligned to maize genome v2 by psRobot 1.2
Genome_build: AGPv2
Supplementary_files_format_and_content: text file include reads and counts of each sRNA
|
| |
|
| Submission date |
Jul 06, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Yong-Xin Liu |
| E-mail(s) |
yxliu@genetics.ac.cn
|
| Organization name |
Institute of Genetics and Developmental Biology, Chinese Academy of Sciences
|
| Department |
State Key Laboratory of Plant Genomics
|
| Lab |
Yang Bai’s lab
|
| Street address |
No.1 Beichenxi Road, Chaoyang District
|
| City |
Beijing |
| ZIP/Postal code |
100101 |
| Country |
China |
| |
|
| Platform ID |
GPL9141 |
| Series (1) |
| GSE59101 |
Small RNA expression pattern in multiple inbred lines and their hybrids of maize embryo |
|
| Relations |
| BioSample |
SAMN02903875 |
| SRA |
SRX647219 |
