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| Status |
Public on Jul 30, 2024 |
| Title |
iPSC, NEFLg1, biol rep 2 |
| Sample type |
SRA |
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| Source name |
induced pluripotent stem cells
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| Organism |
Homo sapiens |
| Characteristics |
tissue: induced pluripotent stem cells
cell line: WTC-NGN2
cell type: iPSC
genotype: WT
treatment: Cas9-NEFLg1 VLP
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Quick-RNA™ Microprep Kit (cat. #R1050).
Using 500 ng of total RNA, we prepared the mRNA libraries using the QuantSeq 3’ mRNA-Sequencing Library FWD V1 Prep Kit (cat. #015.96). After cDNA synthesis, we used 17 PCR cycles to amplify the libraries. Following bead purification, mRNA concentrations were determined by Qubit and fragment lengths were quantified using High Sensitivity d5000 Reagents (cat. #5067-5593) on the Agilent TapeStation 4200. We normalized our libraries to 8.25 nM for pooling and sequenced through single-end sequencing on the Illumina NovaSeqX 10B flow cell with read lengths 101x12x24 (Read 1, Index 1, Index 2).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq X |
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| Description |
harvested 1 d post transduction
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| Data processing |
Sequencing reads were trimmed using CutAdapt (DOI:10.14806/ej.17.1.200) and aligned using HISAT2 (DOI:10.1038/s41587-019-0201-4), and then a read count matrix was generated using featureCounts (DOI: 10.1093/bioinformatics/btt656).
Assembly: hg38
Supplementary files format and content: tab-delimited text file contains raw counts for each sample
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| Submission date |
Jul 22, 2024 |
| Last update date |
Jul 30, 2024 |
| Contact name |
Gokul Nathan Ramadoss |
| E-mail(s) |
gokul.n.ramadoss@gmail.com
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| Phone |
4808097918
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| Organization name |
UCSF
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| Lab |
Conklin Lab
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| Street address |
1200 Mariposa St
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| City |
San Francisco |
| State/province |
California |
| ZIP/Postal code |
94107 |
| Country |
USA |
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| Platform ID |
GPL34281 |
| Series (1) |
| GSE272812 |
Neuronal DNA repair reveals strategies to influence CRISPR editing outcomes |
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| Relations |
| BioSample |
SAMN42743424 |
| SRA |
SRX25415178 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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