|
| Status |
Public on Jun 25, 2020 |
| Title |
input-DNA_1 |
| Sample type |
SRA |
| |
|
| Source name |
thyroid carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: thyroid carcinoma
chip antibody: none
|
| Treatment protocol |
Nuclei were treated with NaCNBH3 and subsequently the binding buffer of Genejet PCR purification kit.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were obtained with lysis buffer and subjected to sonication. DNA-histone complexes were isolated with antibody.
Libraries were prepared according to the protocol of VAHTSTM Universal DNA Library Prep Kit for Illumina® V3.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Raw fastq reads were deduplicated with FastUniq, trimmed by Trim Galore(v0.5.0) to remove adapters and low quality bases, and mapped to the human reference genome GRCh38.p7 using Bowtie2(v 2.3.4.2). Reads with mapping quality less than 10 were discarded by SAMtools(v0.1.19). HOMER was employed for peak calling.
Genome_build: GRCh38
Supplementary_files_format_and_content: peak file, including peak coordiante, fold change, etc.
|
| |
|
| Submission date |
Jun 26, 2019 |
| Last update date |
Jun 25, 2020 |
| Contact name |
Weiwu Zeng |
| E-mail(s) |
zengweiwu@whu.edu.cn
|
| Organization name |
Wuhan University
|
| Department |
College of Chemistry and Molecular Sciences
|
| Street address |
Bayi Road
|
| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430072 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE133336 |
Reversible 5-formyluracil DNA-histone crosslinks: formation and biological effects |
|
| Relations |
| BioSample |
SAMN12142084 |
| SRA |
SRX6367746 |
