NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM4051495 Query DataSets for GSM4051495
Status Public on Apr 24, 2023
Title high MNase-seq T4 R1
Sample type SRA
 
Source name H1299 cells
Organism Homo sapiens
Characteristics hours post infection: 4 hpi
mnase concentration: 600U
Extracted molecule genomic DNA
Extraction protocol H1299 cells infected with Ad were digested at 0, 0.5, 1, 2 and 4 hpi with 100U/600U of MNase for 4/5 min at 37°, denoted as ‘low’/’high’ MNase. After fragmented DNA has been separated on 1.3% agarose gels, mono-nucleosomal fractions were isolated
Library preparation was accomplished using the NEBNext DNA library prep Master Mix Kit (Nex England Biolabs) according to the manufacturers protocol.
 
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina HiSeq 2000
 
Data processing Paired-end reads were mapped to the reference using bowtie2-aligner with following paramters: --very-sensitive-local, --no-discordant
Reads were filtered to mapping quality > 30 and only reads mapped in proper pair were kept using samtools.
Fragments mapped to the Adenovirus reference with a maximum insert size of 139 bp were selected and used for pVII positioning analysis
pVII positions were called using the DANPOS2 toolkit. First, a pVII occupancy profile for each sample was generated and normalized to 20,000 reads using the dpos function with following parameters: -u 1e-5; -a 1; -z 5; -p 0.001, --extend 35 and --mifrsz 0. Next, the profiles were normalized by a genome wide quantile normalization to the first replicate at 0 hpi of each MNase condition (high/low) using the wiq script. Finally, pVII positions were obtained from the normalized pVII occupancy profiles using the dpos function with following parameters: -jd 50; -q 10; -z 5; -a 1.
Genome_build: hg19 and AY339865.1 (adapted)
Supplementary_files_format_and_content: biwig and bed files were generated using DANPOS2 toolkit. bigwig files represent normalized pVII occupancy and bed files are called pVII positions
 
Submission date Aug 28, 2019
Last update date Apr 24, 2023
Contact name Uwe Schwartz
E-mail(s) uwe.schwartz@ur.de
Organization name University of Regensburg
Department NGS Analysis Center
Street address Universitätstraße 32
City Regensburg
ZIP/Postal code 93053
Country Germany
 
Platform ID GPL11154
Series (2)
GSE136548 Changes in adenoviral chromatin organization precede early gene activation [MNase-seq]
GSE136550 Changes in adenoviral chromatin organization precede early gene activation
Relations
BioSample SAMN12647313
SRA SRX6769661

Supplementary file Size Download File type/resource
GSM4051495_high_MNase_TP_4_0h_R1.bw 157.0 Kb (ftp)(http) BW
GSM4051495_high_MNase_TP_4_0h_Replica_1.bed.gz 5.4 Kb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap