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Sample GSM5462975

Query DataSets for GSM5462975

Status

Public on Jul 03, 2024

Title

NC_2

Sample type

SRA

Source name

Floral organ

Organism

Prunus sibirica

Characteristics

cultiva: Prunus sibirica clone
tissue: Floral organ
group: weak frost resistance clone
developmental stage: Blooming stage

Extracted molecule

total RNA

Extraction protocol

Select the natural frost-damaged Prunus sibirica flower organs, use the kit method to extract RNA, and use the Illumina sequencing platform to construct a sequencing library to extract RNA
The six RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

The sequencing-obtained raw image data were converted to sequence reads using CASAVA.
The raw data was filtered by R language, and finally the clean reads for subsequent analysis were obtained.
Trinity v2.4.0 program was used to stitch and assemble clean reads of all samples. Redundancy was removed by clustering with Corset hierarchy, The longest transcript of each gene was selected as Unigene for subsequent analysis.
The transcript sequence obtained by splicing with Trinity was used as a reference sequence. RSEM software (version v1.2.15) (bowtie2, mismatch=0) (bowtie2 default parameters, mismatch = 0)was used to compare clean reads of each repeated sample with reference sequences, and the readcount of each gene was counted and compared. FPKM (fragments per kilobase of exon per million mapped fragments) was used to standardize the readcount of genes.
The DEGseq R package (1.12.0) was used for differential expression analyses. The P-value was calculated based on a negative binomial distribution model. P-values was adjusted using the Benjamini-Hochberg mothed (Benjamini and Hochberg, 1995). Genes with an adjusted P-value < 0.05 and log2(Fold change) > 1 were assigned as differentially expressed.
Genome_build: Prunus armeniaca
Supplementary_files_format_and_content: FPKM file includes gene ID and expression for each sample.

Submission date

Jul 20, 2021

Last update date

Jul 03, 2024

Contact name

Shengjun Dong

E-mail(s)

1996500037@syau.edu.cn

Phone

13898127077

Organization name

Shenyang Agricultural University