|
| Status |
Public on Jan 16, 2019 |
| Title |
Ufo1_2_pericarp_2_sRNA |
| Sample type |
SRA |
| |
|
| Source name |
Ufo1-1 expressser, 18 Day-after-pollination pericarp sample 2, batch 2
|
| Organism |
Zea mays |
| Characteristics |
tissue: pericarp
genotype: Ufo1-1 expresser
developmental stage: 18 days after pollination
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Materials were collected and flash frozen in liquid nitrogen. Total RNA was extracted by Tri reagent (Molecular Research Center, Inc.) according to manufacturer's protocol.
Small RNA libraries were constructed with Illumina Truseq small RNA sample preparation kit (RS-200-0012). RNAseq libraries were constructed with Illumina Truseq RNA sample preparation kit (RS-122-2001) . Script-Seq libraries (strand-specific RNAseq) were constructed with Illumina ScriptSeq RNA-seq library preparation kit (SSV21106).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
small RNA
18 Day-after-pollination pericarp
|
| Data processing |
For data processing, the adapter sequences were trimmed from raw sequence reads. The small RNA sequences were further trimmed to the lengths between 18 and 34 nucleotides. RNA-seq sequences were maintained at the length after adapter trimming.
Sequence data processing was conducted using in-house Perl scripts developed by Meyers lab in University of Delaware
Genome_build: maize AGPv3 genome
Supplementary_files_format_and_content: tag count file
|
| |
|
| Submission date |
Jul 27, 2018 |
| Last update date |
Jan 16, 2019 |
| 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 |
GPL15463 |
| Series (1) |
| GSE117782 |
The dominant and poor penetrant phenotypes of the maize mutation Unstable factor for orange1 are caused by DNA methylation changes at a linked transposon |
|
| Relations |
| BioSample |
SAMN09727523 |
| SRA |
SRX4476041 |
