SAMN36987338
External Id
Sichuan University
INSDC center name
2023-08-15T00:00:00Z
INSDC first public
2023-08-15T04:01:03.583Z
INSDC last update
SRS18608376
INSDC secondary accession
live
INSDC status
Human
NCBI submission model
Human.1.0
NCBI submission package
SRS18608376
SRA accession
35
age
2019-12-08
attribute
West China Second University Hospital
biomaterial_provider
2019-12-08
collection_date
DNA was amplified according to the ChIP Sequencing Sample Preparation Guide provided by Illumina using adaptors and primers. Deep sequencing was performed by the Computational Biology Omics Core of the CAS-MPG Partner Institute using Illumina HiSeq X-10 (2 150). ChIP-seq reads were aligned to the human genome using BOWTIE software (bowtie2 version 2.1.0). The aligned reads were filtered to abandon those that exhibited low mapping quality and duplication arising as an artifact of sample amplification or sequencing. Peak calling was analyzed by using MACS2 (version 1.4.2) on the ChIP file against the input file. Genome-wide normalized signal coverage tracks were created by bamCoverage in deepTools (version 3.3.0) and visualized in the Integrative Genomics Viewer (IGV version 2.5.0). Peaks were annotated to the genomic region and the nearest genes within 2 kb of the TSS using the Bioconductor package ChIPSeeker (version 1.16.1). Peaks overlapping by at least 1 nt with unique gene model promoters (3 kb of each unique gene model TSS) were considered promoter located. De novo motif searches of ChIP-seq peaks were performed using Homer (version v4.11.1).
description
China:Sichuan
geo_loc_name
Infertile patient
isolate
46,XY
karyotype
Homo sapiens
http://purl.obolibrary.org/obo/NCBITaxon_9606
organism
Testis
sample_type
male
sex
Testis
tissue
Human sample from Homo sapiens
title