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| Status |
Public on May 01, 2024 |
| Title |
HUDEP-2 TL20804:TL20805 transfected, clone 124, rep 2 |
| Sample type |
SRA |
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| Source name |
HUDEP-2
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HUDEP-2
cell type: human erythroid progenitor
genotype: PVT1 DHS knockout
treatment: untreated
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| Growth protocol |
HUDEP-2 were maintained in Iscove's modified Dulbecco's medium (IMDM) supplemented with 330 μg/mL human holo-transferrin (Sigma), 10 μg/mL recombinant human insulin (Sigma), 2 IU/mL heparin (Sigma), 5% human AB plasma (obtained from Bloodworks Northwest, Seattle, WA), 3 IU/mL EPO, 100 ng/mL SCF, 1 μg/mL doxycycline (Sigma), and 100 units/ml penicillin/streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Approximately 200,000 cells were collected per culture and total RNA was isolated using QIAGEN RNeasy kit per manufacturer's instructions
RNA library was constructed using the Illumina RNA TruSeq Stranded tRNA with Ribo-Zero Globin
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
LN69560
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| Data processing |
Basecalling, RTA v3.4.4
Alignments to GRCh38, star v2.4.2a
Annotation, cufflinks v2.2.1, GENCODE v25
Subread, featureCounts v1.5.1
Assembly: GRCh38
Supplementary files format and content: featureCounts gene counts per sample as gzipped tab-delimited matrix
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| Submission date |
Dec 27, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Jeff Vierstra |
| E-mail(s) |
jvierstra@altius.org
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| Organization name |
Altius Institute for Biomedical Sciences
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| Street address |
2211 Elliot Ave
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| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98121 |
| Country |
USA |
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| Platform ID |
GPL24676 |
| Series (2) |
| GSE252161 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors [RNA-seq] |
| GSE252163 |
Large-scale discovery of potent, compact and lineage specific enhancers for gene therapy vectors |
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| Relations |
| BioSample |
SAMN39152179 |
| SRA |
SRX23045133 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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