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Sample GSM4002556 Query DataSets for GSM4002556
Status Public on Dec 31, 2020
Title Experiment_02_g2G3
Sample type SRA
 
Source name human cell line
Organism Homo sapiens
Characteristics cell type: Hela cells
genotype: XRCC4(-/-)
treatment: XRCC4 knockout
experiment: Experiment_02
Treatment protocol To create a XRCC4(-/-) cell line to block cNHEJ, a gXRCC4 sequence targeting the XRCC4 gene (NCBI RefSeq: NC_000005.10) was annealed, phosphorylated with T4 Polynucleotide Kinase (New England Biolabs) and cloned into the BsmBI digested LenticrisprV2 plasmid (Addgene). The plasmid was delivered into HeLa cells by lentiviral transduction.
Growth protocol HeLa (ATCC® CCL-2™) cells obtained from the ATCC and LentiX293T (Clonetech) were grown in Dulbecco modified Eagle’s Medium (DMEM) supplemented with 10% Fetal Bovine Serum (HyClone). To assess DNA repair, HeLa cells (0.6 million) were seeded and after one day, co-transfected with a NHEJ reporter plasmid with either pairs of TALEN reporter constructs. Media was changed after 6 hours and cultured in complete media (DMEM+ 10% FBS), with or without mirin.
Extracted molecule total RNA
Extraction protocol The cells post 48 hours transfection were harvested and RNA was extracted using Zymogen RNA prep kit (Zymogen).
The RNA sample library preparation and sequencing on the Illumina platform PE150 was performed at Novagene Corporation Inc.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description Hela cells with only blocking C-NHEJ pathway by XRCC4 knockout in Experiment_02
all_sample_human_RNA_max.txt
Data processing Sequenced reads were imported into CLC Genomics Workbench 12.0 (https://www.qiagenbioinformatics.com/) and trimmed for adaptor sequence using quality limit of 0.05 calculated from a modified-Mott trimming algorithm, read through adapter trimming, and trimming of ambiguous bases from read regions with more than 2 ambiguous reads.
RNA seq analysis was performed with the RNA Seq Analysis tool in Genomics Workbench which is based upon the ENRAGE pipeline2. Default settings were used including a mismatch cost of 2, insertion and deletion cost of 3.
Read 1 and read 2 from pairs could be processed independently as technical replicates.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include read counts for each raw read file
 
Submission date Aug 01, 2019
Last update date Dec 31, 2020
Contact name Martin Schiller
E-mail(s) martin.schiller@unlv.edu
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
 
Platform ID GPL24676
Series (1)
GSE135274 Transcriptome changes of Hela cells with blocking classical and alternative non-homologous end-joining (NHEJ) pathways
Relations
BioSample SAMN12423344
SRA SRX6639247

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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