|
| Status |
Public on Apr 18, 2023 |
| Title |
M_2_0_A |
| Sample type |
SRA |
| |
|
| Source name |
Inflorescence (flower bud)
|
| Organism |
Chrysanthemum x morifolium |
| Characteristics |
tissue: Inflorescence (flower bud)
genotype: M2
treatment: stage 0
|
| Treatment protocol |
Diameter sizes per stage: stage 0, 0.5–2 mm; stage 1, 2-3 mm; stage 2, 3–5 mm; stage 3, 5–6 mm; stage 4, 7–10 mm; and stage 5, 10– 25 mm
|
| Growth protocol |
Plants were grown under greenhouse conditions
|
| Extracted molecule |
total RNA |
| Extraction protocol |
flower buds were sampled, put in liquid nitrogen and RNA was isolated using CTAB/LiCl
Illumina TruSeq® Stranded mRNA sample preparation kit for low-input with an imput of 2,5 µg RNA per sample. Elution 2 for three minutes instead of eight and enrichment PCR for 13 cycles instead of 15.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Mapping and quantification were done using RSEM and Bowtie2 as a mapper
Differential expression analysis was done in R using DESeq2, performing the nbinomWaldTest and only focusing on genes with a maximum 0.01 padj value
Assembly: V1_clustered_reference.fasta -> Reference sequences used for mapping the reads were constructed using Trinity de novo assembly of all read pairs of V1 using default settings. Reference sequences used for mapping the reads were constructed using Trinity de novo assembly of all read pairs of V1 using default settings.
Supplementary files format and content: csv file with per sample read counts
|
| |
|
| Submission date |
Mar 10, 2023 |
| Last update date |
Apr 18, 2023 |
| Contact name |
Annemarie Castricum |
| E-mail(s) |
annemarie_castricum@hotmail.com
|
| Phone |
+31610099554
|
| Organization name |
Wageningen university and research
|
| Department |
Bioscience
|
| Lab |
Plant Developmental Systems (PDS)
|
| Street address |
Droevendaalsesteeg 4
|
| City |
Wageningen |
| State/province |
Gelderland |
| ZIP/Postal code |
6708PB |
| Country |
Netherlands |
| |
|
| Platform ID |
GPL33243 |
| Series (1) |
| GSE227133 |
Differential expression analysis of a Chrysanthemum mutant with an increased percentage of disc florets. |
|
| Relations |
| BioSample |
SAMN33716709 |
| SRA |
SRX19636248 |
