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| Status |
Public on Feb 25, 2019 |
| Title |
WL17 |
| Sample type |
SRA |
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| Source name |
LN229 GBM cell line
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| Organism |
Homo sapiens |
| Characteristics |
cell source: glioblastoma
cell line: LN229
cell type: stable cell line
treatment: ln229 NO-IR 12h
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| Treatment protocol |
For radiation treatment, cells were seeded in complete medium on petri dish at a density of 5x10E4/cm2 24 hours before the treatment. The cells were then exposed to γ-ray once using a GammaCell 220 Cobalt 60 irradiator (Nordion International) with indicated doses. After irradiation, the medium was replaced with fresh complete medium.
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| Growth protocol |
LN229 cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum and 1% Antibiotic-Antimycotic Solution at 37oC with 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Trizol (Thermo Fisher Scientific) by following the manufacture’s manual instruction.
The cDNA libraries were prepared using the NEXTflex™ Illumina Rapid Directional RNA-Seq Library Prep Kit (BioO Scientific) as per the manufacturer’s instructions. Briefly, polyA RNA was purified from 100 ng of total RNA using oligo (dT) beads. The extracted mRNA fraction was subjected to fragmentation, reverse transcription, end repair, 3’– end adenylation, and adaptor ligation, followed by PCR amplification and SPRI bead purification (Beckman Coulter). The unique barcode sequences were incorporated in the adaptors for multiplexed high-throughput sequencing. The final product was assessed for its size distribution and concentration using BioAnalyzer High Sensitivity DNA Kit (Agilent Technologies). Pooled libraries were diluted to 2 nM in EB buffer (Qiagen) and then denatured using the Illumina protocol. The denatured libraries were diluted to 10 pM by pre-chilled hybridization buffer and loaded onto a TruSeq Rapid flow cell on an Illumina HiSeq 2500 and run for 50 cycles using a single-read recipe according to the manufacturer's instructions.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
ln229 NO-IR 12h-2
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| Data processing |
Sequencing data were analyzed using Strand NGS (Version 3.2). Briefly, reads were aligned to reference human genome and annotation file (GRCh38, build 38, RefSeq genes and transcripts, 2017_01_13). One-way ANOVA was performed using p-value threshold=0.05. For Hierarchical clustering analysis, genes showing changes above 2 folds were used. For ingenuity pathway analysis, 1.8-fold was used as the cut-off of downregulated genes, whereas 2-fold was used for upregulated genes. Direct relationships were chosen. For upstream analysis, the p-value cut-off is 0.01.
Genome_build: GRCh38, build 38, RefSeq genes and transcripts, 2017_01_13
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| Submission date |
Oct 17, 2018 |
| Last update date |
Feb 25, 2019 |
| Contact name |
Wei Li |
| E-mail(s) |
weili@pennstatehealth.psu.edu
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| Phone |
7175310003
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| Organization name |
Penn State Hershey College of Medicine
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| Street address |
500 University Drive, PO Box 850, MC H085
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| City |
Hershey |
| State/province |
PA |
| ZIP/Postal code |
17033 |
| Country |
USA |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE121422 |
Inhibition of TAZ contributes radiation-induced senescence and growth arrest in glioma cells |
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| Relations |
| BioSample |
SAMN10254595 |
| SRA |
SRX4900967 |
| 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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