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Sample GSM5776998 Query DataSets for GSM5776998
Status Public on Sep 27, 2022
Title T19_4x_2m_NP40_(20210920_TB_Mv_T19_2_4xMnase_TM2_NP40)
Sample type SRA
Source name MNase-seq of T19 2 NP40
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
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
BioSample SAMN24722815
SRA SRX13655687

Supplementary file Size Download File type/resource
GSM5776998_T19_4x_2m_NP40.fragments.bed.gz 28.7 Mb (ftp)(http) BED
GSM5776998_T19_4x_2m_NP40.normalized_counts.bedgraph.gz 2.2 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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