|
| Status |
Public on Dec 27, 2020 |
| Title |
WT ERF |
| Sample type |
SRA |
| |
|
| Source name |
HUDEP-2
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HUDEP-2
cell type: umbilical cord blood cells derived
genotype: WT
chip antibody: ERF (ab153726, Abcam)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and ERF-DNA complexes were isolated with antibody.
ChIP-seq libraries were prepared for sequencing using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
All clean reads passed quality control with FASTQC and were mapped onto hg19 with bowtie2.
After removal of duplicates with picard, the bam data were ranked, and an index was created with samtools.
We used MACS2 to generate peak calls with input as the control and set a 200-bp band width in the shifting model to denote the peak with p < 0.01.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: *bdg.tdf: tdf files were generated using the MACS.
|
| |
|
| Submission date |
Nov 01, 2020 |
| Last update date |
Dec 27, 2020 |
| Contact name |
Xiuqin Bao |
| E-mail(s) |
wzj1990@i.smu.edu.cn
|
| Organization name |
Southern Medical University
|
| Street address |
No. 1838, Guangzhou avenue north, baiyun district, Guangzhou
|
| City |
Guangzhou |
| ZIP/Postal code |
510515 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE160602 |
Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia [ChIP-seq] |
| GSE160603 |
Epigenetic inactivation of ERF reactivates γ-globin expression in β-thalassemia |
|
| Relations |
| BioSample |
SAMN16621607 |
| SRA |
SRX9415789 |
