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| Status |
Public on Sep 22, 2023 |
| Title |
PBMCs, WARS1, 24h, 2 |
| Sample type |
SRA |
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| Source name |
Peripheral blood mononuclear cells
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| Organism |
Homo sapiens |
| Characteristics |
time: 24 hours
cell type: Peripheral blood mononuclear cells
genotype: WT
treatment: WARS1
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| Treatment protocol |
WARS1 (50 nM) for 24 h
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| Growth protocol |
PBMCs were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% streptomycin & penicillin with 5% CO2 at 37 ℃
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| 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).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| 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
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| Submission date |
Sep 13, 2023 |
| Last update date |
Sep 22, 2023 |
| Contact name |
Mirim Jin |
| E-mail(s) |
mirimj@gachon.ac.kr
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| Organization name |
Gachon University
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| Street address |
155, Gaetbeol-ro
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| City |
Incheon |
| ZIP/Postal code |
21999 |
| Country |
South Korea |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE243125 |
Transcriptome analysis of differentially expressed genes by tryptophanyl-tRNA synthetase 1 in human peripheral blood mononuclear cells |
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| Relations |
| BioSample |
SAMN37386177 |
| SRA |
SRX21772052 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7779601_Row_counts_WARS1_2.txt.gz |
495.6 Kb |
(ftp)(http) |
TXT |
| GSM7779601_TPM_WARS1_2.txt.gz |
458.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
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