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Sample GSM3317121

Query DataSets for GSM3317121

Status

Public on Sep 30, 2022

Title

Input control Monkey 3 (1)

Sample type

SRA

Source name

dissected testis

Organism

Macaca fascicularis

Characteristics

tissue: testis
cell type: male germline cells
antibody: none

Extracted molecule

genomic DNA

Extraction protocol

Testis samples were placed on ice and cut into pieces with sterile scalpel. Homogenates were individually filtered through thwo mesh wire gauzes to remove large pieces of tissue fragments and the cells of stroma. Cells in filtered homogenates were extensively washed with cold PBS and fixed with 1% EM-grade formaldehyde/PBS for 15 min. Crosslinking was quenched with glycine (0.125M final concentration). Cells were centrifuged, resuspended in PBS/1 x proteinase inhibitor cocktail /10% glycerol, and kept at -80 degrres C. A modified ChIP version named ChEP (chromatin enriched for proteomics) was used to precipitate proteins of interest with specific antibodies.
DNA fragments were end-repaired and A-tailed according to Illumina protocol, and then ligated with adapters. DNA fragments that have adapter molecules on both ends were amplified by PCR. DNA concentration of the resulting sequencing libraries was measured with the Qubit 2.0 fluorometer dsDNA HS Assay (Thermo Fisher Scientific), while the size distribution was analyzed using Agilent BioAnalyzer 2100 (Agilent). Paired-end sequencing was performed using an Illumina HiSeq system with Illumina-provided protocols for paired-end sequencing.

Library strategy

ChIP-Seq

Library source

genomic

Library selection

ChIP

Instrument model

HiSeq X Ten

Description

control

Data processing

Paired end reads (R1 and R2 FASTQ files) were treated as single reads
R1 and R2 reads were combined and aligned using bowtie-1.2.2 software with parameters: -best -m 5 -v 3 -5 10 -3 20
Peak calling was done with MACS2-2.1.1. software using a corresponding chromatin input file as a control
Peak calling was applied to the full genome assembly, including assembled chromosomes, and both placed and unplaced fragments
Bedgraph files were conversted to bigWig files using bedGraphToBigWig script (ucsC utilities), excluding chromsome fragments
Genome_build: macFas5 (June 2013), Accession GCA_000364345.1 , NCBI Assembly 704988
Supplementary_files_format_and_content: bigWig file is an indexed binary format file that displays continuous signal data as a graph.

Submission date

Aug 01, 2018

Last update date

Sep 30, 2022

Contact name

Alexander V. Strunnikov

E-mail(s)

alexstrunnikov@gmail.com

Organization name

GIBH

Lab

Molecular Epigenetics