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Status |
Public on Jun 27, 2019 |
Title |
YY1_RBM25-KD ChIP-seq rep1 |
Sample type |
SRA |
|
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Source name |
HepG2
|
Organism |
Homo sapiens |
Characteristics |
cell line: HepG2 cell type: Hepatocellular carcinoma chip antibody: YY1 (Proteintech Cat# 66281-1-lg)
|
Biomaterial provider |
ATCC (HB-8065)
|
Growth protocol |
ENCODE cell culture protocols
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Nuclei were isolated and sonicated and lysates were cleared-up and applied for purification of RBP-DNA complexes with antibodies. Libraries were constructed according to the instruction of the Illumina Preparing Samples for ChIP Sequencing.
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|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
HiSeq X Ten |
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|
Description |
ChIP-seq data (PE)
|
Data processing |
ChIP-seq data were processed in accordance with ENCODE uniform transcription factor ChIP-seq pipeline (https://www.encodeproject.org/chip-seq/transcription_factor/). Briefly, ChIP-seq reads were aligned to the GRCh37 human genome using BWA; PCR duplicates and reads of low quality were filtered; Peak-calling was performed with SPP and IDR with 0.02 IDR threshhold; Signal tracks were generated with MACS2 and bigWig applications from UCSC genome browser (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) Genome_build: GRCh37 (hg19) Supplementary_files_format_and_content: Peak files were narrowPeak files generated by SPP; column information of narrowPeak file is explicated at the link (https://genome-euro.ucsc.edu/FAQ/FAQformat.html#format12).
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|
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Submission date |
Sep 18, 2018 |
Last update date |
Jun 28, 2019 |
Contact name |
Rui Xiao |
E-mail(s) |
xiaorui9@whu.edu.cn
|
Organization name |
Wuhan University
|
Department |
Medical Research Institute
|
Lab |
RNA Biology Lab
|
Street address |
Medical Research Institute, Wuhan University
|
City |
Wuhan |
State/province |
Hubei |
ZIP/Postal code |
430071 |
Country |
China |
|
|
Platform ID |
GPL20795 |
Series (2) |
GSE120104 |
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription [ChIP-Seq] |
GSE120110 |
Pervasive Chromatin-RNA Binding Protein Interactions Enable RNA-based Regulation of Transcription |
|
Relations |
BioSample |
SAMN10082005 |
SRA |
SRX4708117 |