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Sample GSM6261737

Query DataSets for GSM6261737

Status

Public on Jun 25, 2022

Title

THP-1 cells, shDNMT3B, DMSO, replicate1

Sample type

SRA

Source name

Blood

Organism

Homo sapiens

Characteristics

tissue: Blood
cell line: THP-1
cell type: acute myeloid leukemia cell line
genotype: DNMT3B knockdown
treatment: DMSO

Extracted molecule

total RNA

Extraction protocol

RNA was extracted using TruSeq Stranded mRNA Sample Prep Kit (Illumina)
mRNA molecules were purified and fragmented from 0.1-1 ug of total RNA using oligo (dT) magnetic beads. Fragmented mRNAs were synthesized as single-stranded cDNAs through random hexamer priming. Double-stranded cDNA was prepared by using this cDNA as a template for second strand synthesis. After a sequential process of end repair, A-tailing, and adpter ligation, cDNA libraries were amplifed using PCR.

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NovaSeq 6000

Description

shDNMT1_PMA-1

Data processing

Low-quality reads were filtered based on the following criteria: reads containing more than 10% of skipped bases (marked as ‘N’s), reads containing more than 40% of bases with quality scores of less than 20, and reads with average quality scores for each read of less than 20.
The filtering process was performed using in-house scripts. Filtered reads were mapped to the reference genome related to the species using the aligner STAR v.2.4.0b.
Gene expression levels were measured using Cufflinks v2.1.1 and the gene annotation database of the species. For differentially expressed gene (DEG) analysis, gene-level count data were generated using HTSeq-count v0.6.1p1. Based on the calculated read count data, DEGs were identified using the R package ‘TCC’.
The normalization factors were calculated using the iterative DEGES/edgeR method. The Q-value was calculated based on the P-value using the p.adjust function of the R package, with default parameter settings. The DEGs were identified based on a Q-value threshold of less than 0.05 for correcting errors caused by multiple testing.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts for each sample

Submission date

Jun 22, 2022

Last update date

Aug 04, 2022

Contact name

Junyoung Park

E-mail(s)

[email protected]

Organization name

Chung-Ang University

Department

Department of Life Science