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| Status |
Public on Apr 24, 2023 |
| Title |
AsCas12f-WT-PDCD1-rep2 |
| Sample type |
SRA |
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| Source name |
embryonic kidney
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| Organism |
Homo sapiens |
| Characteristics |
tissue: embryonic kidney
cell line: HEK293T
cell type: Kidney epithelial
genotype: Wild type
treatment: Nucleofection
ascas12f version: WT
guide rna_target: PDCD1
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| Growth protocol |
HEK293T cells were purchased from (ATCC, CRL11268) were cultured in DMEM (Gibco 11995) supplemented with 10% (v/v) fetal bovine serum (Gibco), 1% penicillin and streptomycin (Gibco, 15140).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using Purelink Genomic DNA Mini Kit (Thermo Fisher, K1820)
1 µg gDNA was applied to fragmentation, end-repair, A-tailing, adapter ligation, and dsODN-specific amplification, following the published GUIDE-seq protocol.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Description |
GUIDE-seq
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| Data processing |
GUIDE-seq was analysed using an open-source guideseq software: https://github.com/aryeelab/guideseq.
Assembly: hg19
Supplementary files format and content: read density that can be used for visualization on genome browsers.
Library strategy: GUIDE-seq
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| Submission date |
Mar 16, 2023 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Tong Wu |
| E-mail(s) |
tongwu@uchicago.edu
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| Organization name |
University of Chicago
|
| Street address |
929 E 57th St. GCIS E335
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| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
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| Platform ID |
GPL30173 |
| Series (1) |
| GSE211600 |
Off-target effect of engineered AsCas12f variants |
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| Relations |
| BioSample |
SAMN33785778 |
| SRA |
SRX19690775 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7102152_guide-seq.30-e-WT-2.q1.UCSC.bedgraph.gz |
10.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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