|
| Status |
Public on Jan 10, 2022 |
| Title |
small RNA_ms32_1_5mm_r1 |
| Sample type |
SRA |
| |
|
| Source name |
Whole anthers, provided by Walbot lab at Stanford, fromms32-ref sterile sibling ZPP109-6
|
| Organism |
Zea mays |
| Characteristics |
tissue: Dissected whole anthers
genotype: ms32-ref
Stage: 1.5 mm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRI Reagent® (Sigma-Aldrich) follow instruction from manufacturer
For sRNA library preparation, 20- to 30-nt RNAs were excised from a 15% polyacrylamide/urea gel, and ~25 ng of sRNA used for library construction with NEBNext® Small RNA Library Prep Set for Illumina® (New England Biolabs, lnc.) were used for ultra-low amount of total RNA starting from 100 ng. For RNA-seq, 2 µg of total RNA was treated with DNase I (New England BioLabs) and then cleaned with RNA Clean and Concentrator-5 (Zymo Research). The NEBNext® UltraTM II Directional RNA Library Prep Kit for Illumina® (New England BioLabs) was used for library construction with 500 ng of treated RNA.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
sRNA-seq, ms32-ref sterile anther, 1.5 mm, replicate 1
|
| Data processing |
Small RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the small RNA sequences were trimmed to the lengths between 15 and 34 nucleotides. Small RNA reads were mapped to the maize genome (Maize Genome Database).
RNA-seq: the adapter sequences were trimmed from raw sequence reads, and then the RNA sequences were trimmed to the lengths of 50 nucleotides. RNA-seq reads were mapped to the maize genome (Maize Genome Database).
Genome_build: version 4 of the B73 maize genome
Supplementary_files_format_and_content: Text containing distinct RNAs with their raw abundance after removing the adapter sequences
|
| |
|
| Submission date |
Jun 01, 2021 |
| Last update date |
Jan 10, 2022 |
| Contact name |
Blake C. Meyers |
| E-mail(s) |
bmeyers@danforthcenter.org
|
| Phone |
314-587-1422
|
| Organization name |
Donald Danforth Plant Science Center
|
| Lab |
Meyers lab
|
| Street address |
975 N Warson Road
|
| City |
St. Louis |
| State/province |
MO |
| ZIP/Postal code |
63132 |
| Country |
USA |
| |
|
| Platform ID |
GPL17628 |
| Series (1) |
| GSE175915 |
bHLH cascade regulate 24-nt phasiRNA biogenesis in maize anther |
|
| Relations |
| BioSample |
SAMN19489464 |
| SRA |
SRX11040991 |
