|
| Status |
Public on Dec 21, 2019 |
| Title |
SEC28˚C_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Embryonic callus 28˚C
|
| Organism |
Picea abies |
| Characteristics |
location: 11:18:1:1
tissue: Embryonic callus
temperature: 28C
|
| Treatment protocol |
Embryonic calli were treated in each temperature for 3 weeks and then immediately frozen by liquid nitrogen.
|
| Growth protocol |
Needles were harvested in May and August. Pollen was harvested in May. Embryonic calli were grown in dark 22˚C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted as previously described in Gambino et al., 2008. Subsequently, sRNAs were separated from high molecular weight RNAs by PEG8000 as previously described in Peng et al. 2014
Libraries were constructed using the Illumina NEBNext® Small RNA Library Prep Set according to the manufacturer's protocol.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
small RNA
|
| Data processing |
3' adapter (5′ -AGATCGGAAGAGCACACGTCT-3′) sequences were trimmed after removing low quality reads by fastq_quality_filter (-q 20 -p 80 -Q 33). Transfer RNA-, ribosomal RNA-, and small nuclear (nucleoar) RNA-derived sequences were subtracted using bowtie with allowing maximum 1 mismatch. 17–28 nt length reads were extracted and scored.
Genome_build: Pabies1.0-genome-gene-only
Supplementary_files_format_and_content: tab-delimited text files (column1:sequence, column2:read count)
|
| |
|
| Submission date |
Apr 05, 2019 |
| Last update date |
Dec 21, 2019 |
| Contact name |
Miyuki Nakamura |
| E-mail(s) |
[email protected]
|
| Organization name |
Swedish University of Agricultural Sciences
|
| Street address |
Ulls Grand1
|
| City |
Uppsala |
| ZIP/Postal code |
75007 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL19695 |
| Series (1) |
| GSE129413 |
Profiling of small RNA in Norway spruce embryonic calli and male gametophytes |
|
| Relations |
| BioSample |
SAMN11352038 |
| SRA |
SRX5648395 |
