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| Status |
Public on May 18, 2019 |
| Title |
ssODN rep2 |
| Sample type |
SRA |
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| Source name |
DNA donor template, single-stranded oligodeoxynucleotides
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| Organism |
Homo sapiens |
| Characteristics |
tissue: blood
cell type: CD34+ PBSCs
treatment: ssODN
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| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were resuspended in RLT buffer+ β-ME following manufacture protocol (RNEasy Micro kit, Qiagen, Venlo, Netherlands), and snap frozen in LN2 to be stored at -80ºC until RNA extraction (RNEasy Micro kit, Qiagen, Venlo, Netherlands)
RNA-Seq libraries were prepared using the Universal Plus mRNA-Seq kit (NuGEN Technologies Redwood City, CA)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Description |
cpm.txt
ssODN.2
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| Data processing |
RNA sequencing reads were aligned to the reference mouse genome (hg38) using STAR (Dobin et al., 2013).
Raw expression levels were quantified for all annotated genes (Ensembl 92).
Raw expression levels were normalized to CPM values (counts-per-million) using edgeR (Robinson et al., 2010)
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text file include CPM values for all samples
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| Submission date |
May 17, 2019 |
| Last update date |
May 20, 2019 |
| Contact name |
Yerbol Z. Kurmangaliyev |
| Organization name |
University of California, Los Angeles
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| Street address |
675 Charles E. Young Drive South
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| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90095 |
| Country |
USA |
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| Platform ID |
GPL21290 |
| Series (1) |
| GSE131387 |
Editing the Sickle Cell Disease Mutation in Primary Human Hematopoietic Stem Cells: Comparison of Endonucleases and Homologous Donor Templates |
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| Relations |
| BioSample |
SAMN11667710 |
| SRA |
SRX5853069 |
| 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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