|
| Status |
Public on Mar 31, 2023 |
| Title |
WT 6h 1Gy I18_1044_07_3866 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
tissue: Fetal cortices
age: embryonic day 11, 6 hours post 1Gy irradiation
genotype: wild type
|
| Treatment protocol |
Pregnant dams at E11 were given a single dose of whole-body radiation (1 Gy), by using an X-Strahl 320 kV (0.13 Gy/min, inherent filtration: 3 mm of Be, additional filtration: 3.8 mmAl + 1.4 mm Cu + DAP, tube voltage: 250 kV, tube current: 12 mA, sample distance: 100 cm, beam orientation: vertical) in accordance to ISO 4037. Control mice were taken as well to the radiation facility but were not placed within the radiation field (sham-irradiation).
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| Growth protocol |
All the mice were housed under standard laboratory conditions with 12-h light/dark cycle. Food and water were available ad libitum. Female mice were coupled during a 2-h time period in the morning, at the start of the light phase (07:30 am) in order to ensure synchronous timing of embryonic development. The morning of coupling was counted as E0.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fetal cortices were dissected and stored in RLT Plus lysis buffer (Qiagen) at -80°C until RNA extraction using the RNeasy Mini Kit (Qiagen). RNA quality was determined using the RNA nano assay on a 2100 Bioanalyzer (Agilent Technologies). All samples had RNA Integrity Numbers >9.10.
Triplicate RNA-Seq libraries were prepared according to the TruSeq stranded mRNA protocol (Illumina). Briefly, 200 ng of total RNA was purified using poly-T oligo-attached magnetic beads to end up with poly-A containing mRNA. The poly-A tailed mRNA was fragmented and cDNA was synthesized using SuperScript II and random primers in the presence of Actinomycin D. cDNA fragments were end repaired, purified with AMPure XP beads, A-tailed using Klenow exo-enzyme in the presence of dATP. Paired end adapters with dual index (Illumina) were ligated to the A-tailed cDNA fragments and purified using AMPure XP beads. The resulting adapter-modified cDNA fragments were enriched by PCR using Phusion polymerase as followed: 30 s at 98°C; 15 cycles of 10 s at 98°C, 30 s at 60°C, 30 s at 72°C; 5 min at 72°C. PCR products were purified using AMPure XP beads and eluted in 30 µl of resuspension buffer. One microliter was loaded on an Agilent Technologies 2100 Bioanalyzer using a DNA 1000 assay to determine the library concentration and for quality check.
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| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
WT 6h 1Gy
Reads were quality trimmed and mapped to the reference genome GRCm38 (mm10), the expression was normalized to Reads Per Kilobase of exon model per Million (RPKM).
I18_1044_07_3866
|
| Data processing |
Illumina Casava software used for basecalling.
Reads were quality trimmed and good quality reads were mapped to the reference genome GRCm38 (mm10) with the RNA-Seq Analysis toolbox within CLC Genomics Workbench v11.0.1 (Qiagen Co., Ltd.) using the default parameters.
The expression was normalized to Reads Per Kilobase of exon model per Million (RPKM) by dividing the total exon reads over the mapped reads (in millions) and exon length (in kilobase). Differential expression analysis was performed between the samples’ genome mapped reads using CLC differential analysis for RNAseq tool box, using ANOVA like analysis. Differentially expressed genes (DEGs) were generated based on a false discovery rate - corrected p-value (FDR) <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
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| |
|
| Submission date |
Nov 15, 2019 |
| Last update date |
Mar 31, 2023 |
| Contact name |
Mohamed Mysara |
| E-mail(s) |
mohamed.mysara@sckcen.be, mohamed.mysara@gmail.com
|
| Phone |
0032014332836
|
| Organization name |
Belgian nuclear research center (SCK-CEN)
|
| Street address |
Boeretang 200
|
| City |
Mol |
| State/province |
Belgium |
| ZIP/Postal code |
2400 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE140464 |
p53 drives premature neuronal differentiation in response to acute DNA damage during early neurogenesis |
|
| Relations |
| BioSample |
SAMN13292110 |
| SRA |
SRX7156574 |
