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| Status |
Public on Apr 26, 2024 |
| Title |
CLL, SpiD3 1uM, rep2 |
| Sample type |
SRA |
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| Source name |
B-cell
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| Organism |
Homo sapiens |
| Characteristics |
tissue: B-cell
cell line: OSU-CLL
cell type: CLL
treatment: 1 uM SpiD3
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| Treatment protocol |
OSU-CLL cells were treated with SpiD3 (1, 2 μM) or DMSO for 4 h
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| Growth protocol |
OSU-CLL cell lines were cultured in RPMI-1640 with 2 mM L-glutamine, supplemented with 100 U/mL penicillin/100 μg/mL streptomycin, and 10% heat-inactivated fetal bovine serum
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| Extracted molecule |
total RNA |
| Extraction protocol |
OSU-CLL cells (1.5e6 cells/mL) were collected for RNA extraction using the miRNeasy Mini Kit (Qiagen) according to manufacturer instructions
Samples were prepared using the Universal Plus mRNA-Seq with NuQuant kit
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
D1_2
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| Data processing |
For each sample, quality control was assessed by the Fragment Analyzer Automated CE System.
Sequenced reads were mapped using HISAT2 version 2.1.0 to genome build hg38, guided by ENSEMBL GRCh38.99 transcript annotations.
TPM and FPKM normalized values were obtained by Stringtie version 2.1.1.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts and expression values for every gene and every sample
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| Submission date |
Jun 30, 2023 |
| Last update date |
Apr 26, 2024 |
| Contact name |
Jordan Rowley |
| E-mail(s) |
[email protected]
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| Organization name |
University of Nebraska Medical Center
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| Street address |
3828 Jones St, Apt 202
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| City |
Omaha |
| State/province |
NE |
| ZIP/Postal code |
68105 |
| Country |
USA |
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| Platform ID |
GPL21697 |
| Series (1) |
| GSE236239 |
Novel spirocyclic dimer, SpiD3, targets critical tumor survival pathways and displays potent preclinical activity in B-cell chronic lymphocytic leukemia |
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| Relations |
| BioSample |
SAMN36173873 |
| SRA |
SRX20850170 |
| 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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