|
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
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|
|
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 |