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Series GSE132725 Query DataSets for GSE132725
Status Public on Jul 25, 2019
Title Transcriptome and ribosome profiling of XRN1-null HEK293T human cell line generated by CRISPR/Cas9 gene editing
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary XRN1 is the major cytoplasmic exoribonuclease in eukaryotes, which degrades deadenylated and decapped mRNAs in the last step of the 5′–3′ mRNA decay pathway. Metazoan XRN1 interacts with decapping factors coupling the final stages of decay. Ribosome profiling revealed that XRN1 loss impacts not only on mRNA levels but also on the translational efficiency of many cellular transcripts likely as a consequence of incomplete decay. We compared differentially expressed genes derived from the analysis of the transcriptome and the translatome of HEK293T wild-type (WT) and XRN1-null cells by RNA-Seq and Ribo-Seq, respectively. Two biological replicates of each cell line were analyzed. The RNA-Seq analysis indicated that a substantial fraction of the total 10,105 genes showed significant differences between the two cell lines. 2,906 genes were significantly upregulated whilst 2,900 genes were downregulated using a fold change >0 on log2 scale with an FDR<0.005 to determine abundance. Significantly fewer genes showed differences between the WT and the XRN1-null cells at the level of translation with 433 genes showing an increase in abundance of ribosomal footprints whilst 560 genes were decreased as indicated by the Ribo-Seq analysis. Comparative analysis of translational efficiency (TE) in WT and XRN1-null cells on a genome-wide scale as a ratio of ribosomal occupancy to mRNA abundance identified an increase in TE for 102 genes but a decrease for 598 genes with most of the genes showing no evidence of change in the TE.
Overall design Two cell types with two biological replicates analysed using two methods.
Contributor(s) Weber R, Valkov E
Citation(s) 31340047
Submission date Jun 13, 2019
Last update date Jul 25, 2019
Contact name Eugene Valkov
Phone 497071601357
Organization name Max Planck Institute for Developmental Biology
Department Biochemistry
Lab Abt. II
Street address Max-Planck-Ring 5
City Tuebingen
State/province Baden-Wuerttemberg
ZIP/Postal code 72076
Country Germany
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (8)
GSM3890764 Wild-type replicate 1 for RNA-seq
GSM3890765 Wild-type replicate 2 for RNA-seq
GSM3890766 XRN1-null replicate 1 for RNA-seq
BioProject PRJNA548813
SRA SRP201395

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Supplementary file Size Download File type/resource
GSE132725_Final_DE_combined_RNAseq_vs_Riboseq_wt_vs_XRN1.txt.gz 720.0 Kb (ftp)(http) TXT
GSE132725_Final_table_readcounts_RNAseq_vs_Riboseq.txt.gz 202.8 Kb (ftp)(http) TXT
GSE132725_TE_XRN1.txt.gz 578.5 Kb (ftp)(http) TXT
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