|
| Status |
Public on Mar 18, 2024 |
| Title |
JI92, Seed Coat, DevStage 2, replication 2 [SC_JI92.2.2] |
| Sample type |
SRA |
| |
|
| Source name |
seed coat
|
| Organism |
Pisum sativum |
| Characteristics |
tissue: seed coat
developmental stage: DevStage 2
genotype: JI92
|
| Treatment protocol |
no specific treatment to plants, well watered and fertilized, minimalization of stress conditions
|
| Growth protocol |
glasshouse grown plants (spring period of February-June), UP Olomouc, CZ in 5 liters pots with substrate
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using PureLink™ Plant RNA Reagent (Invitrogen). Residual DNA was removed by Baseline-ZERO DNase (Epicenter) treatment followed by phenol/chloroform extraction.
Library preparation started with QC of RNA by Nanodrop, Agarose gel electrophoresis RNA degradation and contamination test and Agilent 2100 integrity checks and quantification. mRNA from organisms was enriched using oligo(dT) beads. Fragmentation of mRNA was done by fragmentation buffer. The cDNA is synthesized by using mRNA template and random hexamers primer and a custom second-strand synthesis buffer with dNTPs, RNase H and DNA polymerase I. Finally, series of terminal repair, A ligation and sequencing adaptor ligation were performed. cDNA library was completed through size selection and PCR enrichment.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
gene_count_pea_dormancy.csv
fpkm_pea_dormancy.csv
|
| Data processing |
Raw sequence reads were cleaned with adapter quality trimming process using BBDuk from BBTools (minlen=25 qtrim=rl trimq=10 ktrim=r k=23 mink=11 hdist=1 tpe tbo)
Sequences were mapped to reference sequence using HISAT2 v2.1.0
Reference sequence-guided assembly was performed using StringTie v2.1.0
Genotype transcripts were compared with reference transcripts using gffcompare
Merging all transcripts from all samples was performed using StringTie v2.1.0.
Read count was done by StringTie v2.1.0 using prepDE.py script
Normalization of genes count to FPKM values were performed using Ballgown v2.20.0 R package.
Assembly: Cameor v1a
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file includes FPKM normalized counts for all samples
|
| |
|
| Submission date |
Oct 10, 2023 |
| Last update date |
Mar 18, 2024 |
| Contact name |
Oldrich Trneny |
| E-mail(s) |
trneny.oldrich@gmail.com
|
| Organization name |
Agricultural research Ltd.
|
| Street address |
Zahradni 1
|
| City |
Troubsko |
| ZIP/Postal code |
66441 |
| Country |
Czech Republic |
| |
|
| Platform ID |
GPL32857 |
| Series (1) |
| GSE244961 |
Domestication has altered gene expression in pea seed coat |
|
| Relations |
| BioSample |
SAMN37749122 |
| SRA |
SRX22043287 |
