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| Status |
Public on Mar 06, 2020 |
| Title |
bfPAM2min |
| Sample type |
SRA |
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| Source name |
PCR fragments; gene EGFP
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| Organism |
synthetic construct |
| Characteristics |
tissue: PCDNA3.1-EGFP
genotype: wild type
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were collected after 48h post-transfection for genomic DNA extraction using FastPure Cell/Tissue DNA Isolation Mini Kit(Vazyme)
Libraries were prepared according to VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme)
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
bfPAMMerged.xlsx
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| Data processing |
The clean data was generated by trimming low quality bases at both ends of read and remove short fragments, this work was completed by sequencing company
For PAM depletion assay, we used custom Python or R scripts to get the result
For guide-seq, the sequencing data was processed by corresponding software named guideseq,the human genome version used in the analysis is hg19;
For deep-seq, the data was handled by CRISPRessoPooled
Genome_build: hg19
Supplementary_files_format_and_content: txt files include DNA sequences for each sample
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| Submission date |
Mar 05, 2020 |
| Last update date |
Mar 06, 2020 |
| Contact name |
chen peng |
| E-mail(s) |
[email protected]
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| Organization name |
Wuhan University
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| Department |
College of Life Sciences
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| Street address |
College of Life Sciences, Wuhan University
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| City |
Wuhan |
| ZIP/Postal code |
430072 |
| Country |
China |
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| Platform ID |
GPL15228 |
| Series (1) |
| GSE146420 |
A Cas12a ortholog with stringent PAM recognition followed by low off-target editing rates for genome editing |
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| Relations |
| BioSample |
SAMN14305645 |
| SRA |
SRX7855744 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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