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Sample GSM6539668 Query DataSets for GSM6539668
Status Public on Sep 27, 2022
Title Dm_NP40_MNase_3_(20210920_TB_Dm_S2_4xMnase_TM2_NP40)
Sample type SRA
 
Source name MNase-seq
Organism Drosophila melanogaster
Characteristics cell type: S2
Extracted molecule genomic DNA
Extraction protocol MNase-extraction_TB2021.pdf
Library_Preparation_TB2021.pdf
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description MNase-seq of Drosophila NP40
Data processing Genome_build: UCSC dm6
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 the paired-end 25bp reads to the reference sequence for Drosophila melanogaster dm6. 2. We extracted properly paired reads from the alignments with bedtools bamtobed to generate a bed file of aligned fragments (Supplementary file fragments.bed.gz). 3. 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 Sep 02, 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 GPL17275
Series (1)
GSE193224 A giant virus genome is densely packaged by stable nucleosomes
Relations
BioSample SAMN30648531
SRA SRX17408764

Supplementary file Size Download File type/resource
GSM6539668_Dm_NP40_MNase_3.fragments.bed.gz 41.7 Mb (ftp)(http) BED
GSM6539668_Dm_NP40_MNase_3.normalized_counts.bigwig 22.2 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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