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| Status |
Public on Jun 20, 2024 |
| Title |
WiT49, actD, 2wk, rep2 |
| Sample type |
SRA |
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| Source name |
WiT49
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| Organism |
Homo sapiens |
| Characteristics |
cell line: WiT49
cell type: Wilms tumor
time: 2wk
treatment: actD
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| Treatment protocol |
WiT49 cells were incubated in complete growth medium with 2nM actD or DMSO for 6 or 72 hours, in three replicates per condition. For 2-week long treatments, WiT49 were maintained and passaged in two 7-day cycles of drug/vehicle-supplemented media for 3 days, followed by no additive complete growth media for 4 days.
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| Growth protocol |
The anaplastic Wilms tumor cell line WiT49 was maintained in Dulbecco’s Modified Eagle Medium (DMEM) with 1000 mg/L glucose, 4mM L-glutamine, 1mM pyruvate supplemented with antibiotic-antimycotic and 10% FBS in 37°C at 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For total RNA sequencing, RNA was extracted using the Direct-zol RNA Miniprep Kit (ZymoResearch R2050) or the miRneasy Mini Kit (Qiagen 217004) according to manufacturer protocols. Ribosome footprints were isolated based on previous publications (McGlincy et al, 2017; Ingolia et al, 2012).
Ttotal RNA sequencing libraries were prepared with the TruSeq Stranded Total RNA LT or TruSeq Stranded Total RNA-seq (Illumina) Sample Prep Kit from Illumina. For ribosome proifiling, rRNA depletion was performed using the Low Input RiboMinus™ Eukaryote System v2, and sequencing libraries were generated using the NEBNext® Small RNA Library Prep Set for Illumina.
ribosome profiling + total RNA seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
wit49_2wkdmso2
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| Data processing |
Trimmed reads from ribosome profiling and RNA sequencing were aligned to the hg38 reference genome using HISAT2.
For ribosome profiling, reads longer than 30 nt were filtered out.
Remaining reads were assembled to GENCODE v26 transcript annotations using StringTie.
Assembly: hg38
Supplementary files format and content: comma-separated text file containing raw counts for each gene for each sample
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| Submission date |
Jun 20, 2024 |
| Last update date |
Jun 21, 2024 |
| Contact name |
Kenneth S Chen |
| E-mail(s) |
kenneth.chen@utsouthwestern.edu
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| Organization name |
UT Southwestern
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| Department |
Pediatrics
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| Street address |
5323 Harry Hines Blvd
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| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE270330 |
Proteasome inhibition sensitizes anaplastic Wilms tumor to actinomycin D |
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| Relations |
| SRA |
SRX24989186 |
| BioSample |
SAMN41934763 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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