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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 18, 2017 |
| Title |
X3 |
| Sample type |
SRA |
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| Source name |
photon irradiation
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| Organism |
mixed sample |
| Characteristics |
tissue: head and neck carcinoma
tissue: Human cells injected in Mice
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| Treatment protocol |
Cell irradiations. Five million cells were seeded onto 12 cm2 tissue culture flasks, 48 h prior to the irradiations, which were carried out at the Centre Antoine Lacassagne, Nice, France (four independent experiments) with either protons (P, 63 MeV Cyclotron MEDICYC, CAL, Nice, France) or photons (X, 6 MeV Dual energy Clinac 21EX Linear Accelerator, Varian Inc., Palo Alto, CA, USA). The cells were irradiated three times, one week apart with 8 Gy, and processed 6h after irradiation. Cells were re-seeded after each irradiation and kept in culture until the next irradiation. After the third irradiation, the cells were expended in culture for three weeks.
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| Growth protocol |
The cells were cultured in Dulbecco's Modified Eagle's Medium supplemented with 7% fetal bovine serum (Thermo Fisher Scientific, Waltham, MA, USA).
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| Extracted molecule |
total RNA |
| Extraction protocol |
One million non-irradiated, P or X irradiated CAL33 cells (CR-MI group) were injected subcutaneously into the flank of 6-week-old NMRI-Foxn1nu/Foxn1nu female mice (Janvier Labs, Le Genest-Saint-Isle, France, n=10/group). The tumor volume (v = L x l2 x 0.52) was determined following measurement with a caliper. When the tumors reached one cm3, the mice were sacrificed and the tumors collected. Total RNA was extracted from tumors with the AllPrep® DNA/RNA/Protein Mini Kit (Qiagen, Hilden, Germany).
Libraries were generated from 1µg of total RNA using Truseq Stranded mRNA kit (Illumina). Libraries were then quantified with KAPA library quantification kit (Kapa biosystems) and pooled. 4nM of this pool were loaded on a Nextseq 500 high output flowcell and sequenced on a NextSeq 500 platform (Illumina) with 2 × 75bp paired-end chemistry
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
photon irradiation
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| Data processing |
Concurential mapping with STAR_2.4.0i versus hg19 and mm10 genome folowing Encode RNA-seq options "--outFilterIntronMotifs RemoveNoncanonicalUnannotated --alignMatesGapMax 1000000 --outReadsUnmapped Fastx --alignIntronMin 20 --alignIntronMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMultimapNmax 20"
FeatureCounts counting (subread-1.5.0-p3-Linux-x86_64) with " --primary -g gene_name -p -s 1 -C" options
Supplementary_files_format_and_content: table_featurecounts.txt: Human and Mouse genes count tables
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| Submission date |
Dec 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
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| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
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| Street address |
660 route des lucioles
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| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
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| Platform ID |
GPL22727 |
| Series (1) |
| GSE90761 |
Whole transcriptomic screening the RNA from control (O), photon radiotherapy (X) and proton therapy (P) tumors |
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| Relations |
| BioSample |
SAMN06093985 |
| SRA |
SRX2388656 |
| 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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