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://www.nibb.ac.jp/potentia/nucleosome/English/e_index.html
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| DRA002604 |
NGS (ChIP-seq, RNA-seq) |
Unrestricted-access | 2016/09/30 |
*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
MOLECULAR DATA
| 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 |
DATA PROVIDER
Principal Investigator: Yasuyuki Ohkawa
Affiliation: Division of Transcriptomics, Medical Institute of Bioregulation, Kyushu university
Funds / Grants (Research Project Number):
| Name | Title | Project 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
| Title | DOI | Dataset 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 |
