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Sample GSM5211121 Query DataSets for GSM5211121
Status Public on May 13, 2024
Title ATMi 1_16h
Sample type SRA
 
Source name fibroblast cells
Organism Homo sapiens
Characteristics cell type: hTERT-immortalized fibroblasts
skin: foreskin
agent: ATMi
brdu antibody: Mouse monoclonal anti-BrdU, Sigma-Aldrich, Cat#B8434
Treatment protocol Cells fully confluent were seeded at 20 % confluence in 150 mm dishes, and grown overnight. Cells were synchronized in the G0/G1 phase in serum starvation medium (DMEM supplemented with 0.2 % FBS, 2mM L-glutamine and penicillin/streptomycin) in 5 % CO2 at 37°C for 26 h, and released into S-phase with regular DMEM for the indicated timepoints. 14h after release cells were treated for 2h with ATM (10 microM) or ATRi (4 microM), while pulsed with BrdU for the last hour. In the case of DMSO, DRB (100 microM) or alpha-amanitin (a-Am, 3 microg/ml), cells were treated 15 h after release for 1 hour.
Growth protocol Human immortalized fibroblasts (BJ-hTERT cells) were cultured in DMEM (Sigma-Aldrich) supplemented with 10 % FBS, 2 mM L-glutamine and penicillin/streptomycin in 5 % CO2 at 37°C.
Extracted molecule genomic DNA
Extraction protocol PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific)
Illumina's Nextera XT DNA Library Preparation Kit following manufacturer’s protocol
paired end on 4 Lanes (L1-L4)
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Description single timepoint analysis
Data processing Library strategy: BrdU-Seq
Paired-end BrdU-seq reads were aligned to the hg38 genome assembly using Bowtie 2 v.2.3.3.1 (Langmead et al., 2012).
BAM files were sorted and indexed using SAMtools v.1.4 (Li et al., 2009).
The reads that mapped to region DAC blacklisted for mappability by the ENCODE project were removed.
Coverage calcualtion was done using the function “quantify” in EaSeq, from the start to the end of the gene of all annotated genes
There are no processed data files for the samples "ATMi 1_16h" "ATMi 2_16h" "ATRi 1_16h" "ATRi 2_16h", as we have used these files only for metagene profiles over specific features
Genome_build: hg38
Supplementary_files_format_and_content: .txt, containing the quantifications over each gene as above described
 
Submission date Mar 25, 2021
Last update date May 13, 2024
Contact name Marco Saponaro
E-mail(s) m.saponaro@bham.ac.uk
Organization name University of Birmingham
Department Institute of Cancer and Genomic Sciences
Street address Vincent Drive
City Birmingham
ZIP/Postal code B15 2TT
Country United Kingdom
 
Platform ID GPL18573
Series (2)
GSE169619 Genome wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression
GSE169620 Genome wide identification of replication fork stalling/pausing sites and the interplay between RNA Pol II transcription and DNA replication progression
Relations
BioSample SAMN18490647
SRA SRX10443210

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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