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Sample GSM7779602 Query DataSets for GSM7779602
Status Public on Sep 22, 2023
Title PBMCs, WARS1, 24h, 3
Sample type SRA
 
Source name Peripheral blood mononuclear cells
Organism Homo sapiens
Characteristics time: 24 hours
cell type: Peripheral blood mononuclear cells
genotype: WT
treatment: WARS1
Treatment protocol WARS1 (50 nM) for 24 h
Growth protocol PBMCs were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% streptomycin & penicillin with 5% CO2 at 37 ℃
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from individual samples and controls using Trizol reagent (Invitrogen) according to the manufacturer’s protocol. Total RNA was then quantitated using a Nanodrop spectrophotometer (Thermo Scientific) and quality assessed using the RNA 6000 Nano assay kit (Agilent) and Bioanalyser 2100 (Agilent).
NGS sequencing libraries were generated from 1 µg of total RNA using a TruSeq RNA Sample Prep Kit (Illumina) according to the manufacturer's protocol.
The resulting cDNA libraries were then paired-end sequenced (2 × 101 bp) for samples with the Novaseq 6000 system (Illumina).
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Data processing Paired end sequence files from eleven samples (Fastq: R1, R2) were obtained and processed using Trimmomatic-0.36 with the following parameter settings: leading: 5, trailing: 5, sliding window: 4:15, and minlen: 36. After quality scoring and assessing the read lengths, RNA-Seq reads were mapped to the human reference genome GRCh38 (Gencode release 12) using STAR with default parameters.
Accurately quantifying the expression level of a gene from RNASeq reads was achieved using RSEM, which assembles individual transcripts from RNA-Seq reads that have been aligned to the genome sequences. Next, TPM was calculated for each transcribed fragment in the sample to quantify the expression level. To compare each sample, TPM underwent global normalization and was used for further analysis. Principal component analysis (PCA) was applied to the obtained gene expression profiles using the R package stats.
The normalized expression profiles of DEGs expressing more than 0.3 TPM and five read counts were used for DEGs analysis using EdgeR. The expression profile of each gene was scaled to a z-score and hierarchically clustered using a complete linkage method. Visualization was achieved using the ggplot2 library in R packages.
Assembly: GRCh38 (Gencode release 12)
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
 
Submission date Sep 13, 2023
Last update date Sep 22, 2023
Contact name Mirim Jin
E-mail(s) mirimj@gachon.ac.kr
Organization name Gachon University
Street address 155, Gaetbeol-ro
City Incheon
ZIP/Postal code 21999
Country South Korea
 
Platform ID GPL24676
Series (1)
GSE243125 Transcriptome analysis of differentially expressed genes by tryptophanyl-tRNA synthetase 1 in human peripheral blood mononuclear cells
Relations
BioSample SAMN37386176
SRA SRX21772053

Supplementary file Size Download File type/resource
GSM7779602_Row_counts_WARS1_3.txt.gz 509.7 Kb (ftp)(http) TXT
GSM7779602_TPM_WARS1_3.txt.gz 460.6 Kb (ftp)(http) TXT
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Raw data are available in SRA

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