|
| Status |
Public on Jun 27, 2019 |
| Title |
PCBP1_ChIP-seq_K562 |
| Sample type |
SRA |
| |
|
| Source name |
K562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: Hepatocellular carcinoma
chip antibody: PCBP1 (MBL Cat# RN024P)
|
| Biomaterial provider |
ATCC (CCL-243)
|
| 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.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
ChIP-seq data (SE)
|
| 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).
|
| |
|
| 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 |
GPL16791 |
| 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 |
SAMN10081930 |
| SRA |
SRX4708075 |
