|
| Status |
Public on Jul 26, 2023 |
| Title |
24 DAP endosperm replicate 3 [88543_END_24_REP3] |
| Sample type |
SRA |
| |
|
| Source name |
endosperm
|
| Organism |
Hordeum vulgare |
| Characteristics |
tissue: endosperm
developmental stage: 24 days after pollination
genotype: Morex
|
| Growth protocol |
Seeds of six-rowed spring barley Hordeum vulgare cv. Morex were germinated for 3 days at 25 ° and then moved into the peat pots containing mixture of soil and sand. Plants were grown in climatic chamber under long-day regime (16 h day 20 °C, 8 h night 16 °C; humidity 60 %). After 10 days plants were transfered into 15 x 15 cm pots containing the same soil and cultivated in the same conditions until flowering.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated using Rneasy(R) Plant Mini Kit (QIAGEN) and Spectrum ™ Plant Total RNA Kit (Sigma-Aldrich) according to the manufacturer's instructions including on-column DNase I (Sigma-Aldrich) treatment and stored at -80 °C until use.
The RNA quality was checked using Bioanalyzer 2100 with RNA 6000 Pico Chips (all Agilent) and samples with RNA integrity number > 6.8 were processed into RNA-Seq mRNA libraries using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® with poly-A selection.
The polyA RNA-enriched libraries were sequenced as single end 100-bp RNA seq reads on the HiSeq2500 instrument (Illumina) at Vienna BioCenter.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
raw_counts.txt
TPM_counts.txt
|
| Data processing |
Illumina RTA3 was used for basecalling and .cbcl files were converted to .fastq using bcl2fastq2 Conversion Software v2.20
Sequenced reads were trimmed for adaptor sequence and low-quality sequence and then mapped to Morex v3 whole genome using hisat2 v2.1.0 with default parameters. Hisat2 output was converted and sorted by samtools view and samtools sort, respectively.
The number of reads falling in the exons of transcripts were counted using subread v1.5.2 with parameters -p -t exon -g Parent.
Transcripts Per Million (TPM) were calculated in R using standard formula.
Assembly: Mascher, Martin, et al. "Long-read sequence assembly: a technical evaluation in barley."The Plant Cell33.6 (2021): 1888-1906.
Supplementary files format and content: Tab-delimited text file including RAW counts for each Sample
Supplementary files format and content: Excel table including RAW counts for each Sample, calculated mean, standard deviation and transcript per million values
|
| |
|
| Submission date |
May 24, 2023 |
| Last update date |
Jul 26, 2023 |
| Contact name |
Ales Pecinka |
| E-mail(s) |
[email protected]
|
| Organization name |
Institute of Experimental Botany of the AS CR
|
| Street address |
Šlechtitelů 31
|
| City |
Olomouc |
| ZIP/Postal code |
77900 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL22077 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN35345543 |
| SRA |
SRX20502053 |
