|
| Status |
Public on Jun 29, 2022 |
| Title |
ovule-2 |
| Sample type |
SRA |
| |
|
| Source name |
ovule
|
| Organism |
Brassica carinata x Brassica rapa |
| Characteristics |
tissue: ovule
developmental stage: meiosis to mature embryo sac formation
genotype: AABBCC
sample type: Brassica allohexaploid (Brassica carinata male × Brassica rape female)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
A total amount of 1-3μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina ® (NR604-01/02 following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Alignment HISAT2 2.1.0 mapping reads to genome
Transcript Assembly StringTie 1.3.2 sequence assembly
Gene Expression Quantity HTSeq 0.6.0 estimating gene expression level
Assembly: B. rapa genome v1.5 sequences, B. nigra genome v1.1 sequences and B.oleracea genome v1.0 sequences (http://brassicadb.cn)
Supplementary files format and content: tab-delimited text files include FPKM values for eachsample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 25, 2022 |
| Last update date |
Jun 29, 2022 |
| Contact name |
Ji Chengyan |
| E-mail(s) |
chengyanji@139.com
|
| Phone |
18567628877
|
| Organization name |
Zhengzhou University
|
| Street address |
100 Science Avenue
|
| City |
Zhengzhou |
| ZIP/Postal code |
450001 |
| Country |
China |
| |
|
| Platform ID |
GPL32203 |
| Series (1) |
| GSE201456 |
Transcriptome Profiling Identified Candidate Genes Contributing to Male and Female Gamete Development in Synthetic Brassica Allohexaploids |
|
| Relations |
| BioSample |
SAMN27763813 |
| SRA |
SRX14990517 |
