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Sample GSM7528591

Query DataSets for GSM7528591

Status

Public on Nov 29, 2023

Title

MN_Initial_3

Sample type

SRA

Source name

flowers

Organism

Camellia reticulata

Characteristics

tissue: flowers
cultivar: Manao

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted using Trizol reagent (Invitrogen) following the manufacturer's protocols, and mRNA was enriched using Oligo(dT) Magnetic Beads. RNA quality was analyzed using Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and RNA concentration was measured using a Qubit 2.0 Fluorometer (Life Technologies, CA, USA). RNA integrity was assessed by Agarose gel electrophoresis.
To prepare the RNA library, RNA was fragmented by the fragmentation buffer. First-strand cDNA was synthesized using N6 random primers, and then the second strand was synthesized to obtain the cDNA. The purified cDNA was modified by end-repair, A-tail, and ligation. After fragment size selection using AMPure XP beads, PCR amplification was performed to obtain the final sequencing library. Finally, all libraries were sequenced on the Illumina HiSeq platform.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

To obtain high-quality reads, Trimmomatic (v0.36) was used to remove reads with adapters and more than 20% of bases with a quality value of less than ten.
Transcripts were assembled using Trinity.
By mapping reads to the transcripts, only transcripts with correlation coefficients between replicate samples ≥ 0.8 were used for the following analysis.
All qualified transcripts were annotated to function databases, including NR, SwissProt, KEGG, and GO databases.
Only transcripts with an expression of ≥ 10 in at least one set of samples were used for subsequent analysis, and the average of the expression of all replicate samples was used as the gene expression.
Assembly: Mixed_camellia.fa
Supplementary files format and content: gene_FPKM.txt: Tab-delimited text file includes FPKM values or each Sample.

Submission date

Jul 03, 2023

Last update date

Nov 29, 2023

Contact name

Yan Qu

E-mail(s)

quyan@swfu.edu.cn

Organization name

Southwest Forestry University

Street address

Kunming