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| Status |
Public on Apr 24, 2023 |
| Title |
low MNase-seq T0 R1 |
| Sample type |
SRA |
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| Source name |
H1299 cells
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| Organism |
Homo sapiens |
| Characteristics |
hours post infection: 0 hpi
mnase concentration: 100U
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| 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.
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| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2000 |
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| 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
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| Submission date |
Aug 28, 2019 |
| Last update date |
Apr 24, 2023 |
| Contact name |
Uwe Schwartz |
| E-mail(s) |
uwe.schwartz@ur.de
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| Organization name |
University of Regensburg
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| Department |
NGS Analysis Center
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| Street address |
Universitätstraße 32
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| City |
Regensburg |
| ZIP/Postal code |
93053 |
| Country |
Germany |
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| 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 |
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| Relations |
| BioSample |
SAMN12647311 |
| SRA |
SRX6769663 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4051497_low_MNase_TP_0_0h_R1.bw |
167.5 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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