|
| Status |
Public on Jul 07, 2020 |
| Title |
shCTRL RNA-Seq Replicate C |
| Sample type |
SRA |
| |
|
| Source name |
AB22 cells plus shCTRL
|
| Organism |
Mus musculus |
| Characteristics |
cell type: AB22
silencing: shCTRL
dose (gy): -
|
| Treatment protocol |
For the silencing of HMGB1, shCTRL-MM and shHMGB1-MM were obtained by infection with pTRIPZ-shCTRL or pTRIPZ-shHMGB1 viral particles at a multiplicity of infection of 20; transduced cells were selected with 4 μg/mL puromycin. Cells were then cultured in RPMI1640, as above, using tetracycline-free FBS (Euroclone). All cells were cultured in humidified incubator at 37°C with 5% oxygen.shRNA expression was induced by adding 1 μM doxycycline (Sigma) to the culture medium. All experiments were performed after 7-10 days from doxycycline addition. For the DSB irradiation treatment, G1-synchronised shCTRL and shHMGB1 MM cells and irradiated them with 0, 3, 5 and 10 Grays from a Caesium137 source.
|
| Growth protocol |
Murine malignant mesothelioma (MM) AB22 cells were obtained from Cell Bank Australia and cultured in RPMI 1640 supplemented with 10% v/v FBS, 2 mM L-glutamine and 100 U/ml penicillin/streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA from G1-synchronized cells was isolated using the NucleoSpin RNA II kit (Macherey-Nagel). Ribosomal RNA was subtracted using RiboMinus Gold TM Technology (ThermoFisher)
Libraries of cDNA were prepared with TruSeq RNA Library Prep Kit (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
trimming with Trimmomatic (v0.32)
alignment with STAR_2.5.3a
counting reads with featureCounts (Gencode M13 annotation)
normalization (Table with log2RPKM Normalized values, with edgeR rpkm() function on TMM normalized)
Genome_build: mm10 GRCm38
|
| |
|
| Submission date |
Jul 24, 2019 |
| Last update date |
Jul 07, 2020 |
| Contact name |
Jose Manuel Garcia-Manteiga |
| E-mail(s) |
garciamanteiga.josemanuel@hsr.it
|
| Organization name |
OSR - San Raffaele Scientific Institute
|
| Department |
Center for Translational Genomics and Bioinformatics
|
| Street address |
Via Olgettina 58
|
| City |
Milan |
| State/province |
-- |
| ZIP/Postal code |
20132 |
| Country |
Italy |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE134795 |
Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (RNA-seq) |
| GSE134798 |
Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells |
|
| Relations |
| BioSample |
SAMN12353737 |
| SRA |
SRX6581648 |
