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Sample GSM5057653

Query DataSets for GSM5057653

Status

Public on Feb 02, 2021

Title

MARC145-mock

Sample type

SRA

Source name

MARC145

Organism

Chlorocebus aethiops

Characteristics

tissue: Fetal kidney
cell type: Epithelial cells
cell line: MARC145
treatment: untreated

Treatment protocol

One replicate was shaan virus infected for 24hours

Growth protocol

MARC145 derived African green monkey kidney origin, was cultured in DMEM(Gibco) supplemented with antibiotic-antimycotic(100 IU/mL penicillin, 100 ug/mL streptomycin, and 0.25 ug/mL amphotericin B, Gibco) and 10% fetal bovine serum(Gibco, USA). HEK-293, A549 and HRT18 cell line derived human kidney, lung and colon origin, was cultured in MEM, F-12k and RPMI1640 media with 10% fetal bovine serum and antibiotic-antimycotic. All cell was maintained routinely by re-plating with 2~3×10^6 cells into cell culture flask (T75) for 3~4 days in each growth medium.

Extracted molecule

total RNA

Extraction protocol

Total RNA was extracted from shaanvirus infected host cells with Trizol LS reagent
The infected cells were harvested at 24 hours post infection, and a total RNA was extracted from the harvested cells with Trizol LS reagent. Total cDNA libraries were prepared from extracted RNA using Illumina TruSeq Stranded Total RNA LT kit according to the manufacturer’s instruction. TruSeq Stranded Total RNA Sample Prep Guide, Part #15031048 Rev. E. Samples were sequenced on NovaSeq 6,000 platform.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Data processing

Raw sequences were checked the quality of the data with FastQCv0.11.7 program before proceeding.
The adapter sequence was removed with Trimmomatic 0.38 program. Trimmed data was generated by removing base qulity less than 3 from reads ends and base unsatisfied with window size =4, mean quality =15 using the sliding window trim method.
cDNA fragment were mapped GRCh37 or Chlorocebus_sabeus_1.1_NCBI_100 genomic DNA reference with Bowtie 2 2.3.4.1 aligner.
The mapped reads were assembled with the known gene/transcript with StringTie version 2.1.3b program.
The amount of abundance of the transcript was normalized FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value considering read count, transcript length and depth of coverage.
Statistical analysis for each comparision combination was processed with fold change, exactTest using edgeR. Significant results were selected under the condition |fc|>=2 & exactTest raw p-value<0.05.
Genome_build: Chlorocebus_sabeus_1.1_NCBI_100

Submission date

Feb 01, 2021

Last update date

Feb 02, 2021

Contact name

Jiyeong Noh

E-mail(s)

wldud1540@gmail.com

Organization name

Chungbuk National University

Street address

Chungdae-ro 1