GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE135274 Query DataSets for GSE135274
Status Public on Dec 31, 2020
Title Transcriptome changes of Hela cells with blocking classical and alternative non-homologous end-joining (NHEJ) pathways
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: The recombinant endonucleases introduce double-strand breaks (DSBs) in genomic DNA at targeted sites and non-homologous end-joining (NHEJ) pathways repair the breaks introducing indels into the genome. To investigate whether there is another NHEJ pathway or if A-NHEJ and C-NHEJ are redundant, we examined NHEJ edits in HeLa cells.
Methods: To test among these possibilities, we engineered a NHEJ reporter system using targeted TALEN induced double strand DNA breaks. C-NHEJ was blocked in XRCC4(-/-) cells and A-NHEJ was blocked pharmacologically with mirin. To assess how NHEJ was maintained, differentially expressed genes were determined by RNA-Seq.
Results: When both C-NHEJ and A-NHEJ are blocked, edits were still observed. No changes in expression of DNA repair genes was observed. However, when both NHEJ pathways were blocked, genes from several pathways including DNA damage response, hypoxic response, chromatin packaging, p53 response and two genes that stimulate homologous recombination were differentially expressed.
Conclusions: NHEJ is maintained when both NHEJ pathways are blocked through a transcriptional response that must compensate for the inhibited steps in both pathways.
Overall design Overall design: Total eight samples separated in two experiments (biological duplicates) were sequenced, for profiling transcriptomes of Hela cells under four conditions – 1) Hela cells, 2) Hela cells with only blocking C-NHEJ pathway by XRCC4 knockout, 3) Hela cells with only blocking A-NHEJ pathway by mirin treatment, and 4) Hela cells with blocking both C-NHEJ and A-NHEJ pathways.
Contributor(s) Benjamin R, Schiller MR
Citation(s) 35054780
Submission date Aug 01, 2019
Last update date Jan 31, 2022
Contact name Martin Schiller
Organization name University of Nevada, Las Vegas
Department Nevada Institute of Personalized Medicine
Street address 4505 S Maryland Pkwy
City Las Vegas
State/province NV
ZIP/Postal code 89154
Country USA
Platforms (1)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (8)
GSM4002552 Experiment_01_g2G3
GSM4002553 Experiment_01_g2G3_M
GSM4002554 Experiment_01_gSCR
BioProject PRJNA558142

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE135274_all_sample_human_RNA_max.txt.gz 909.4 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap