|
| Status |
Public on Jul 07, 2020 |
| Title |
shHMGB1 ATAC-Seq |
| Sample type |
SRA |
| |
|
| Source name |
AB22 cells plus shHMGB1
|
| Organism |
Mus musculus |
| Characteristics |
cell type: AB22
silencing: shHMGB1
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 |
genomic DNA |
| Extraction protocol |
ATACseq protocol is described in Buenrostro et al, 2015. Permeabilised cells are incubated with Tn5 from Illumina to tagment chromatin. Genomic DNA is purified using Quiagen MinElute PCR Purification kit.
Libraries are prepared from tagmented genomic DNA following the protocol described in Buenrostro et al, 2015.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
trimming with Trimmomatic (v0.32)
alignment with bwa mem (v0.7.5-r404)
remove duplicates with MarkDuplicates
filtering for Paired Unique, quality, autosomic plus sex chromosome (samtools view -F 3844 -f 2 -q 15)
filtering out blacklist (From Encode with intersectBed -v)
peak calling (MACS2 callpeak -q 0.05 --extsize 73 --nomodel --shift 73 --nolamda)
Nucleosome calling with NucleoATAC (v0.3.4)
Genome_build: mm10 GRCm38
Supplementary_files_format_and_content: narrowPeak called by MACS on sorted filtered bam files
Supplementary_files_format_and_content: occ, nfr and nuc positioning bed and bedgraph calculated by NucleoATAC
|
| |
|
| 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) |
| GSE134796 |
Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (ATAC-seq) |
| GSE134798 |
Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells |
|
| Relations |
| BioSample |
SAMN12353728 |
| SRA |
SRX6581653 |
