|
| 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 |
