NBDC Research ID: hum0016.v1

 

SUMMARY

Aims: To elucidate the mechanism of chromatin formation in human sperm cells.

Methods: Analysis of ChIP-seq data of the testis-specific histone variant H3.5 (with H3.3 as control) and RNA-seq data in testis cells

Participants/Materials: Normal testis cells

URL: http://nucleosome.kyushu-u.ac.jp/English/e_index.html

 

Data Set IDType of DataCriteriaRelease Date
DRA002604

NGS

(ChIP-seq, RNA-seq)

Un-restricted Access 2016/09/30

*Release Note

 

MOLECULAR DATA

DRA002604

Participants/Materials: Normal human testis cells
Targets

IP with specific antibody for H3.3 and H3.5 (ChIP-seq),

Input data (whole genome), and RNA-seq data (whole genome)

Target Loci for Capture Methods -
Platform Illumina HiSeq 1500
Library Source gDNA and total RNA extracted from human testis cells
Cell Lines -
Library Construction (kit name)

NEBNext Ultra DNA Library Prep Kit for Illumina (ChIP-seq)

NEBNext Ultra Directional RNA Library Prep Kit for Illumina (RNA-seq)

Fragmentation Methods

MNase (ChIP-seq)

NEBNext Ultra Directional RNA Library Prep Kit (RNA-seq)

Spot Type Single-end
Read Length (without Barcodes, Adaptors, Primers, and Linkers) 50 bp (depth: 0.5-0.8)
DDBJ Sequence Read Archive ID DRA002604
Total Data Volume 15 GB
Comments (Policies) NBDC policy

*When the research results including the data which were downloaded from NHA/DRA, are published or presented somewhere, the data user must refer the papers which are related to the data, or include in the acknowledgment. Learn more

 

DATA PROVIDER

Principal Investigator: Yasuyuki Ohkawa

Affiliation: Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu university

Funds / Grants (Research Project Number):

NameTitleProject Number

KAKENHI Grant-in-Aid for Scientific Research on Innovative Areas

(Research in a proposed research area: Dynamic chromatin structure and function)

Exploring chromatin dynamics in cell differentiation 25116010
     

 

PUBLICATIONS

TitleDOIData Set ID
1 Histone H3.5 forms an unstable nucleosome and accumulates around transcription start sites in human testis doi: 10.1186/s13072-016-0051-y DRA002604
2