|
| Status |
Public on Sep 27, 2022 |
| Title |
T19_30min_MNase_(20210506_TB_Mv_20min_0430) |
| Sample type |
SRA |
| |
|
| Source name |
MNase-seq of T19 30 min MNase
|
| Organism |
Marseillevirus marseillevirus |
| Characteristics |
strain: T19
type: DNA from MNase-digested chromatin
cell type: viral DNA
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
MNase-extraction_TB2021.pdf
|
| |
|
| Library strategy |
MNase-Seq |
| Library source |
genomic |
| Library selection |
MNase |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Genome_build: T19_genome.fasta
1. We used Bowtie2 2.4.2 with options "--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700" to map 25bp paired-end reads to the reference sequence (Drosophilia melanogaster dm6 or Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 2. We extracted properly paired reads from the alignments to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz). 3. We used bedtools genomecov to make a normalized count bedgraph file. Normalized counts are the fraction of counts at each base pair scaled by the size of the reference sequence so that if the scaled counts were uniformly distributed there would be 1 at each position (Supplementary file normalized_counts.bedgraph.gz).
|
| |
|
| Submission date |
Jan 07, 2022 |
| Last update date |
Sep 29, 2022 |
| Contact name |
Jorja Henikoff |
| E-mail(s) |
jorja@fhcrc.org
|
| Phone |
206-667-4850
|
| Organization name |
Fred Hutchinson Cancer Research Center
|
| Department |
Basic Sciences
|
| Lab |
Henikoff
|
| Street address |
1100 Fairview AV N, A1-162
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98109-1024 |
| Country |
USA |
| |
|
| Platform ID |
GPL31187 |
| Series (1) |
| GSE193224 |
A giant virus genome is densely packaged by stable nucleosomes |
|
| Relations |
| BioSample |
SAMN24722826 |
| SRA |
SRX13655756 |
