← All datasets

GSE122425

GSE GEO
View on GEO Export SRA CSV

Effects of NSUN2 deficiency on the mRNA 5-methylcytosine modification and gene expression profile in HEK293 cells (RNA-Seq)

Organism: Homo sapiens
Platform: GPL11154
Samples: 6
Experiment Types:
Expression profiling by high throughput sequencing
Submitted: Nov 12 2018
Last Updated: Mar 27 2019
Status: Public on Nov 16 2018
Contact: Zhen,,Sun (Yangzhou University)

Relations

BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA505172 SRA: https://www.ncbi.nlm.nih.gov/sra?term=SRP168405

Summary

Aim: To study the biological function of NSUN2 in regulating gene expression and cell proliferation. Materials & methods: The NSUN2 gene was knocked down in HEK293 cells via CRISPR/Cas9 system. Gene expression were assessed using RNA-Seq. Results: A total of 790 differentially expressed genes (DEGs) were identified.

Overall Design

mRNA profiles of wild type (WT) and NSUN2-/- HEK293 cells were generated by deep sequencing, in triplicate.

Analysis (5 steps)

View Data Processing
Processing steps for GSE122425
  1. Bcl2fastq (v2.17.1.14) used for basecalling.
  2. 3’ adaptor-trimming and low quality reads removing by Cutadapt（version 1.9.1）
  3. The high quality trimmed reads (clean reads) were aligned to the human reference genome (UCSC HG19) using Hisat2(v2.0.1).
  4. Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using Htseq (V0.6.1).
  5. Differential expression analysis used the DESeq2 (V1.6.3).

Supplementary Files (2)

GSE122425_Group_293-VS-293-NK_DE_significant_anno.xlsx Download
GSE122425_all.counts.293_vs_293NK.edgeR_all.xls.gz Download
GEO Samples (6)
GSM3466389 GSM3466390 GSM3466391 GSM3466392 GSM3466393 GSM3466394

SRA Experiments (6) and Runs (6)

Total: 28048 MB
SRX5001092 SRP168405 RNA-Seq PAIRED
GSM3466389: WT rep1; Homo sapiens; RNA-Seq
Sample: SRS4035809
BioProject: PRJNA505172
BioSample: SAMN10411694
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: kidney
strain: HEK293
passages: 8-12
Original files (1)
kidney
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8181090 50113273 15033981900 4233.71 SRR8181090, SRR8181090.sralite SRA
SRX5001093 SRP168405 RNA-Seq PAIRED
GSM3466390: WT rep2; Homo sapiens; RNA-Seq
Sample: SRS4035810
BioProject: PRJNA505172
BioSample: SAMN10411693
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: kidney
strain: HEK293
passages: 8-12
Original files (1)
kidney
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8181091 51025077 15307523100 4346.12 SRR8181091, SRR8181091.sralite SRA
SRX5001094 SRP168405 RNA-Seq PAIRED
GSM3466391: WT rep3; Homo sapiens; RNA-Seq
Sample: SRS4035811
BioProject: PRJNA505172
BioSample: SAMN10411692
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: kidney
strain: HEK293
passages: 8-12
Original files (1)
kidney
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8181092 55578364 16673509200 4766.49 SRR8181092, SRR8181092.sralite SRA
SRX5001095 SRP168405 RNA-Seq PAIRED
GSM3466392: NSUN2-KO rep1; Homo sapiens; RNA-Seq
Sample: SRS4035812
BioProject: PRJNA505172
BioSample: SAMN10411691
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: kidney
strain: HEK293
passages: 8-12
Original files (1)
kidney
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8181093 55985951 16795785300 4745.06 HEK293NK-SEQ1_combined_R1.fastq.gz, HEK293NK-SEQ1_combined_R2.fastq.g… SRA
SRX5001096 SRP168405 RNA-Seq PAIRED
GSM3466393: NSUN2-KO rep2; Homo sapiens; RNA-Seq
Sample: SRS4035813
BioProject: PRJNA505172
BioSample: SAMN10411690
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: kidney
strain: HEK293
passages: 8-12
Original files (1)
kidney
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8181094 57970846 17391253800 4926.25 HEK293NK-SEQ2_combined_R1.fastq.gz, HEK293NK-SEQ2_combined_R2.fastq.g… SRA
SRX5001097 SRP168405 RNA-Seq PAIRED
GSM3466394: NSUN2-KO rep3; Homo sapiens; RNA-Seq
Sample: SRS4035814
BioProject: PRJNA505172
BioSample: SAMN10411689
Platform: ILLUMINA
Instrument: Illumina HiSeq 2000
Organism: Homo sapiens
Sample attributes
source_name: kidney
strain: HEK293
passages: 8-12
Original files (1)
kidney
Runs (1)
Run Spots Bases Size (MB) Files Link
SRR8181095 59817973 17945391900 5029.97 HEK293NK-SEQ3_combined_R1.fastq.gz, HEK293NK-SEQ3_combined_R2.fastq.g… SRA

Linked Publications (1)

Multiplexed transcriptome discovery of RNA-binding protein binding sites by antibody-barcode eCLIP.
Nature methods · 2023

Data Files (6)

Accession File Name Stored Type Output Type Mapping Assembly Size Download
— HEK293NK-SEQ1_combined_R1.fastq.gz RNA-Seq 4.6 GB link
— HEK293NK-SEQ2_combined_R1.fastq.gz RNA-Seq 4.8 GB link
— HEK293NK-SEQ3_combined_R1.fastq.gz RNA-Seq 4.9 GB link
— SRR8181090 RNA-Seq 4.1 GB link
— SRR8181091 RNA-Seq 4.2 GB link
— SRR8181092 RNA-Seq 4.7 GB link