|
| Status |
Public on Mar 23, 2022 |
| Title |
ME_2_0mm, replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
LCM isolated meiocytes
|
| Organism |
Zea mays |
| Characteristics |
tissue: Isolated meiocytes from fixed 2.0 mm maize anthers
genotype: W23 inbred
Stage: 2.0 mm
|
| Treatment protocol |
Anthers were dissected from tassels and then measured using a micrometer (Fisher Scientific).
|
| Growth protocol |
Maize (Zea mays) W23 bz2 inbred line plants were grown in Stanford, CA, USA under greenhouse conditions (31℃/21℃, 14 h day/10 h night light cycle with supplemental LED and UV-A lamps providing ~50% of summer sun conditions).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from three different LCM cell samples and FA samples at 1.5 mm and 2.0 mm using the RNAqueous™-Micro Kit (Invitrogen).
RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
NextSeq 550 |
| |
|
| Description |
LCM isolated meiocytes from fixed 2.0 mm anthers of W23 inbred maize, provided by Walbot lab at Stanford
For small RNA library preparation, RealSeq®-AC kits (SomaGenics) were used for ultra-low amounts of total RNA starting with 100 ng from whole anthers or 1 to 10 ng from LCM cell samples. Sequencing in a single-end mode on an Illumina NextSeq (University of Delaware) yielded 75 bp reads for sRNA-seq.
|
| 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).
Genome_build: version 4 of the B73 maize genome
|
| |
|
| Submission date |
Aug 19, 2021 |
| Last update date |
Mar 23, 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 |
GPL27775 |
| Series (1) |
| GSE182476 |
24-nt phasiRNAs move from tapetal to meiotic cells in maize anthers |
|
| Relations |
| BioSample |
SAMN20863907 |
| SRA |
SRX11828788 |
