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| Status |
Public on Oct 16, 2018 |
| Title |
Cpf1-BE-3 |
| Sample type |
SRA |
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| Source name |
293FT cells
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| Organism |
Homo sapiens |
| Characteristics |
cell line: 293FT
type: DNA
treatment: Cpf1-BE
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| 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).
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| 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.
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| 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.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Description |
5'-end trimming of R1: 1 - 5
3'-end trimming of R1: 131-150
CDKN2A, DNMT1, DYRK1A, FANCF, RUNX1, Site4 Cpf1-BE DNA repllicate 3
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| 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
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| Submission date |
Oct 16, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Li Yang |
| E-mail(s) |
[email protected]
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| Organization name |
Fudan University
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| Department |
Institutes of Biological Sciences
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| Street address |
131 Dong-An Road
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| City |
Shanghai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE105002 |
High-fidelity base editing mediated by Cpf1-cytidine deaminase fusion |
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| Relations |
| BioSample |
SAMN07787798 |
| SRA |
SRX3287099 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2813789_Cpf1-BE-3.txt.gz |
333.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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