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Sample GSM8583251

Query DataSets for GSM8583251

Status

Public on Nov 27, 2024

Title

Control3,rep3

Sample type

SRA

Source name

T24

Organism

Homo sapiens

Characteristics

cell line: T24
cell type: Human bladder cancer cells
genotype: Control

Extracted molecule

total RNA

Extraction protocol

RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
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

Description

Control3

Data processing

Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

Submission date

Oct 20, 2024

Last update date

Nov 27, 2024

Contact name

Changxue Liu

E-mail(s)

[email protected]

Organization name

The Affiliated Hospital of Qingdao University

Street address

Qingdao, Shandong, China