|
| Status |
Public on Sep 01, 2021 |
| Title |
776-48h-HH3-bio-rep-2-tech-rep-1 |
| Sample type |
SRA |
| |
|
| Source name |
SV40
|
| Organism |
Betapolyomavirus macacae |
| Characteristics |
strain/background: 776
genotype/variation: WT
time: 48h
virion: No
gradient: none
chip antibody: HH3
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
The samples obtained from ChIP analyses were first purified using Zymo Research ChIP DNA Clean and Concentrator columns according to the supplied protocol.
Libraries were prepared using the New England Biolabs Next UltraII kit according to the protocol supplied with the kit with one exception. All reagent volumes were reduced by half for the preparation of libraries with no apparent effect on library quality or quantity.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina MiSeq |
| |
|
| Data processing |
Preliminary quality control analysis of FastQ files was performed using FastQC v.0.11.2.
The three prime adapters were trimmed from the reads using scythe v0.981. Quality trimming was carried out using sickle v1.33.
To remove contaminating cellular reads, reads aligning to African green monkey (Chlorocebus sabeus1.1) or human (hg19) genomes were removed.
Duplicate fragments were removed using the Picard Tools (Broad) Mark Duplicates function.
Bam files were filtered to contain only fragments between 100-150bp using an awk script.
Replicate bam files were merged together using samtools v1.3.1.
Bedgraphs normalized to 1x Coverage were generated from filtered, deduplicated reads using Deeptools v2.5.4.
Genome_build: GCA_000837645.1 (ViralProj14024)
Supplementary_files_format_and_content: *_depthNorm.bedgraph: BedGraphs normalized to 1x Coverage were generated from deduplicated reads using Deeptools v2.5.4.
|
| |
|
| Submission date |
Oct 31, 2018 |
| Last update date |
Sep 01, 2021 |
| Contact name |
Danielle Perley |
| E-mail(s) |
epi.bio.core@und.edu
|
| Organization name |
University of North Dakota Genomics Core
|
| Street address |
1301 N Columbia Rd
|
| City |
Grand Forks |
| State/province |
North Dakota |
| ZIP/Postal code |
58203 |
| Country |
USA |
| |
|
| Platform ID |
GPL25757 |
| Series (1) |
| GSE122052 |
Genome-wide maps of histone modifications in the SV40 virus |
|
| Relations |
| BioSample |
SAMN10357400 |
| SRA |
SRX4963798 |
