|
| Status |
Public on Dec 24, 2022 |
| Title |
fruit skin (FS) of WT ‘Royal Gala’, biological Sample 2 |
| Sample type |
SRA |
| |
|
| Source name |
fruit skin (FS)
|
| Organism |
Malus domestica |
| Characteristics |
tissue: tissue
age: fruit skin
genotype: WT
|
| Extracted molecule |
total RNA |
| Extraction protocol |
From these tissue samples, RNA was isolated using the Spectrum Plant Total RNA kit (Sigma-Aldrich) according to the manufacturer’s instructions. 5 µg total RNA was used to construct strand-specific poly-A RNA libraries as described by (Haile et al., 2017).
Libraries were sequenced using Novaseq 6000 sequencing system (Illumina) to produce paired-end reads per library ranging from 20 – 27 million. Reads were aligned to the GDDH13 reference genome (Daccord et al., 2017) using Bowtie2 (Langmead and Salzberg, 2012).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
WT_FS_2
WT_FS.txt
|
| Data processing |
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia)
Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.16.1).
Genome_build: https://www.rosaceae.org/jbrowse/index.html?data=data%2Fmalus%2Fmdomestica_gddh13_v1.1&loc=Chr00%3A21091343..31637013&tracks=DNA%2Cgenes%2CmRNA&highlight=
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
|
| |
|
| Submission date |
Apr 26, 2021 |
| Last update date |
Dec 24, 2022 |
| Contact name |
Tiyu Ding |
| E-mail(s) |
[email protected]
|
| Organization name |
Chinese Academy of Agricultural Sciences
|
| Street address |
Hanghai East Road
|
| City |
Zhengzhou |
| State/province |
Henan |
| ZIP/Postal code |
450000 |
| Country |
China |
| |
|
| Platform ID |
GPL29987 |
| Series (1) |
| GSE173297 |
microRNA172 targets APETALA2 to regulate anthocyanin biosynthesis |
|
| Relations |
| BioSample |
SAMN18870763 |
| SRA |
SRX10679707 |
