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Status |
Public on Apr 24, 2023 |
Title |
low MNase-seq T0.5 R1 |
Sample type |
SRA |
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Source name |
H1299 cells
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Organism |
Homo sapiens |
Characteristics |
hours post infection: 0.5 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 |
SAMN12647316 |
SRA |
SRX6769664 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4051498_low_MNase_TP_0_5h_R1.bw |
169.6 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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