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Sample GSM3985937 Query DataSets for GSM3985937
Status Public on Dec 01, 2019
Title GSTS_008: JRy12379_strepSeq_cycling
Sample type SRA
 
Source name streptavidin precipitated chromatin from exponentially growing cells
Organism Saccharomyces cerevisiae
Characteristics strain: JRy12379
growth conditions: cycling in YPD
genotype: H3-Avi TetR-BirA(1-213) / TetR-BirA(214-320) gal10::TetO
preciptation conditions: streptavidin (invitrogen #65001)
Extracted molecule genomic DNA
Extraction protocol Cells were mechanically disrupted, and chromatin was solubilized with Mnase. Chromatin was precipitated using either streptavidin-coupled magnetic beads or a V5 antibody agarose matrix.
NEBNext Ultra II library kit was used with dual index primers to prepare DNA for sequencing
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina MiniSeq
 
Description fig panel: 1b,c
GSTS_008
Data processing Raw reads were mapped to SacCer3 reference genome, modified to include the gal10::TetO sequence. Sequences were aligned using Bowtie2 with parameters -p 16 -N 1 -L 17, and raw reads were trimmed to 38bp for all experiments.
Reads were filtered by insert size to 150bp and 200bp correponding to mononucleosome fragments. Using custom code, each base in the genome was counted for how often it appeared in the sequencing library (NOT how often the base was sequenced, but rather how often each base fell between the ends of a concordantly-aligned paired ned read).
Reads were filtered by insert size to 150bp and 200bp correponding to mononucleosome fragments. Using custom code, read midpoints were extracted and stored as a bedGraph, corresponding to a histogram of read midpoints
Genome_build: SacCer3 (modified)
Supplementary_files_format_and_content: All proccessed data is a BedGraph
 
Submission date Jul 30, 2019
Last update date Dec 02, 2019
Contact name Gavin Schwebs Schlissel
E-mail(s) gschliss@gmail.com
Phone 9256428068
Organization name UC Berkeley
Department Molecular Cell Biology
Lab Rine
Street address 440 Barker Hall
City Berkeley
State/province CA
ZIP/Postal code 94720
Country USA
 
Platform ID GPL22715
Series (1)
GSE135102 The nucleosome core particle remembers its position through DNA replication and transcription
Relations
SRA SRX6614924
BioSample SAMN12413016

Supplementary file Size Download File type/resource
GSM3985937_JRy12379-ypd_S2_L001_R1_001.fastq.gz.sam.bedGraph.gz 57.5 Mb (ftp)(http) BEDGRAPH
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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