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Sample GSM5776935 Query DataSets for GSM5776935
Status Public on Sep 27, 2022
Title 601_12B_MPE_(20210810_TB_601_12B_MPE_210730)
Sample type SRA
Source name MPE-seq of 601 on 12-copy array replicate 2
Organism synthetic construct
Characteristics description: Widom 601 12-copy array with 40-bp linkers
type: DNA from MPE-digested chromatin
cell type: Linear DNA
Extracted molecule genomic DNA
Extraction protocol MPE-extraction_TB2021.pdf
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
Data processing Library strategy: MPE-seq
Genome_build: Genome_601x3.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 GPL19604
Series (1)
GSE193224 A giant virus genome is densely packaged by stable nucleosomes
BioSample SAMN24722878
SRA SRX13655704

Supplementary file Size Download File type/resource
GSM5776935_601_12B_MPE.fragments.bed.gz 1.2 Mb (ftp)(http) BED
GSM5776935_601_12B_MPE.normalized_counts.bedgraph.gz 3.6 Kb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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