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Sample GSM2813815 Query DataSets for GSM2813815
Status Public on Oct 16, 2018
Title Cas9-BE3-1_2+Cas9-BE3-2_2+Cas9-BE3-3_1
Sample type SRA
 
Source name 293FT cells
Organism Homo sapiens
Characteristics cell line: 293FT
type: DNA
treatment: Cas9-BE3
Treatment protocol For base editing in genomic DNA, cells were seeded in a 24-well plate at a density of 200,000 per well and transfected with 500 μl serum-free Opti-MEM that contained 5.04 μl LIPOFECTAMINE LTX (Life, Invitrogen), 1.68 μl LIPOFECTAMINE plus (Life, Invitrogen), 1 μg pCMV-dCpf1-BE0 (pCMV-dCpf1-BE, pCMV-dCpf1-BE-YE, pCMV-dCpf1-BE-YEE, pCMV-dCpf1-eBE, pCMV-dCpf1-eBE-YE, pCMV-BE2 or pCMV-BE3), and 0.68 μg crRNA or sgRNA-expressing plasmid. After 72 hr, the genomic DNA was extracted from the cells with QuickExtractTM DNA Extraction Solution (QE09050, Epicentre).
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 free.
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 5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 106-150
FANCF, RUNX1 Cas9-BE3 DNA replicate 1 and CDKN2A, DYRK1A Cas9-BE3 DNA replicate 2 and DNMT1 Cas9-BE3 DNA replicate 3
Data processing 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 Oct 16, 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)
GSE105002 High-fidelity base editing mediated by Cpf1-cytidine deaminase fusion
Relations
BioSample SAMN07787771
SRA SRX3287125

Supplementary file Size Download File type/resource
GSM2813815_Cas9-BE3-1_2+Cas9-BE3-2_2+Cas9-BE3-3_1.txt.gz 286.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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