NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM2610010 Query DataSets for GSM2610010
Status Public on Aug 29, 2017
Title eBE-S3-3_1+eBE-S3-3_4
Sample type SRA
 
Source name 293FT cells
Organism Homo sapiens
Characteristics cell line: 293FT
treatment: eBE-S3
5'-end trimming of r1: 1 - 5
3'-end trimming of r1: 121 - 150
Treatment protocol For DNA, cells were seeded in a 6-well plate at a density of 8 × 105 per well and transfected with 500 μl serum-free Opti-MEM that contained 5.4 μl LipofectamineTM 2000 (Thermo Fisher Scientific), 2.5 μg pCMV-BE3 (pCMV-eBE3a or pCMV-eBE-S3), 1.6 μg sgRNA-expressing plasmid without or with 50, 100, 200 ng pUGI-NLS. After 24 hr, puromycin (ant-pr-1, InvivoGen) and blasticidin (ant-bl-1, InvivoGen) were added to the media at the final concentration of 10 μg/ml,
Growth protocol 293FT from ATCC were maintained in DMEM (10566, Gibco/Thermo Fisher Scientific) + 10% FBS (16000-044, Gibco/Thermo Fisher Scientific) and have been tested for mycoplasma contamination.
Extracted molecule genomic DNA
Extraction protocol For DNA, 72 hr after transfection, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
For DNA, DNA-seq libraries were prepared with Illumina TruSeq ChIP Sample Preparation Kit. Deep sequencing was performed on Illumina Hiseq 2500 and Hiseq X ten at CAS-MPG Partner Institute for Computational Biology Omics Core, Shanghai, China.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model HiSeq X Ten
 
Description EMX1 eBE-S3 DNA replicate 3 and Site4 eBE-S3 DNA replicate 3
eBE_Indels.xlsx
Data processing Library strategy: DNA-Seq
Basecalling using Illumina Casava1.8.2 software.
High-throughput sequencing reads were separated according to 6-nt experimental barcodes.
Reads were aligned against the GRCh37/hg19 human reference genome using BWA-MEM 0.7.9a-r786.
Genome_build: hg19 for human samples
Supplementary_files_format_and_content: Excel for Indels and Base Subtitutions
 
Submission date May 09, 2017
Last update date May 15, 2019
Contact name Li Yang
E-mail(s) liyang_fudan@fudan.edu.cn
Organization name Fudan University
Department Institutes of Biological Sciences
Street address 131 Dong-An Road
City Shanghai
ZIP/Postal code 200032
Country China
 
Platform ID GPL20795
Series (1)
GSE98685 Enhanced base editing by co-expression of free uracil DNA glycosylase inhibitor
Relations
BioSample SAMN06920508
SRA SRX2792359

Supplementary file Size Download File type/resource
GSM2610010_eBE-S3-3_1+eBE-S3-3_4.xlsx 2.2 Mb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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