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Sample GSM6001434 Query DataSets for GSM6001434
Status Public on Sep 27, 2022
Title 601_Xl_MPE_XL_(20220324_TB_601_MPE_XLnuc_Xlink_cntrl_20220317)
Sample type SRA
Source name MPE-seq of 601 with Xenopus laevis histones, cross-linked
Organism synthetic construct
Characteristics description: DNA from MPE-digested chromatin
Extracted molecule genomic DNA
Extraction protocol MPE-extraction_TB2021.pdf
viral DNA
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
Description Widom 601 3-copy array with 40-bp linkers
Data processing Library strategy: MPE-seq
Genome_build: Genome_601x3.fasta
1. We used cutadapt 2.9 with parameters "--nextseq-trim 20 -m 20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters off 50bp paired-end reads. 2. We used Bowtie2 2.4.2 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the trimmed reads to the reference sequence (Marseillevirus marseillvirus strain T19 or Marseillevirus marseillvirus strain G648 or 3 copies of the artificial sequence Widom 601). 3. We extracted properly paired reads from the alignments with bedtools bamtobed to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz). 4. We used bedtools genomecov to make a normalized count bigwig 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.bigwig).
Submission date Apr 01, 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 GPL19424
Series (1)
GSE193224 A giant virus genome is densely packaged by stable nucleosomes
BioSample SAMN27183534
SRA SRX14697314

Supplementary file Size Download File type/resource
GSM6001434_601_Xl_MPE_XL.fragments.bed.gz 6.5 Mb (ftp)(http) BED
GSM6001434_601_Xl_MPE_XL.normalized_counts.bigwig 34.8 Kb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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