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| Status |
Public on Feb 14, 2024 |
| Title |
IB106 cells, 1Gy-TNs exposition, biol rep 2 |
| Sample type |
SRA |
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| Source name |
Sarcoma
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Sarcoma
cell line: IB106
cell type: Cell line derived from patient sarcoma
treatment: 1Gy-TNs exposition
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| Growth protocol |
Sarcoma cells were harvested with trypsin-EDTA (0.05%, v/v, Thermo Fischer Scientific, Illkirch, France, cat. no 25300062) right away irradiation, and 2000 cells were seeded in a 12-well cell culture plate (CellstarTM, Grenier Bio-one, Dutscher Sas, Bernolsheim, France, cat. no 665180).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was extracted from cells after NPs exposure and/or irradiation using the RNeasy mini kit (Qiagen SAS, Courtaboeuf, France cat. no 74104) according to the manufacturer’s instructions.
Whole-transcriptome cDNA libraries were first constructed from extracted mRNA using a PCR-cDNA barcoding kit (Oxford Nanopore Technologies, Oxford, UK, cat. no SQK-PCB109).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
MinION |
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| Description |
PCR-cDNA barcoding kit on R9.4.1 flowcell
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| Data processing |
guppy v6.1.4 was used to perform high-accuracy base-calling and demultiplexing of the fast5 files
Alignment was performed using minimap2 on the hg38 human transcriptome and read count was extracted using a custom Python script
Supplementary files format and content: comma-separated text file including raw counts for each sample
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| Submission date |
Nov 16, 2023 |
| Last update date |
Feb 14, 2024 |
| Contact name |
Hervé Seznec |
| E-mail(s) |
[email protected]
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| Organization name |
LP2iB
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| Street address |
19 Chemin du Solarium
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| City |
Gradignan |
| ZIP/Postal code |
33170 |
| Country |
France |
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| Platform ID |
GPL24106 |
| Series (1) |
| GSE248011 |
Sarcoma Cell-specific Radiation Sensitization by Titanate Scrolled Nanosheets: Insights from Physicochemical Analysis and Transcriptomic Profiling |
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| Relations |
| BioSample |
SAMN38287273 |
| SRA |
SRX22551441 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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