|
| Status |
Public on Jul 31, 2020 |
| Title |
Fetal_Rep1_CTCF (chip-seq) |
| Sample type |
SRA |
| |
|
| Source name |
Fetal anterior temporal cortex
|
| Organism |
Homo sapiens |
| Characteristics |
developmental stage: Adult
tissue: brain (adult anterior temporal cortex)
chip antibody: CTCF (Abcam, ab70303)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody.
All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
ChIP-seq data were mapped to human reference genome hg19 using Bowtie. The first 36 bases of each read were used for mapping. We only use non-redundant reads to eliminate possible duplicates from biased PCR amplification.
Genome_build: hg19
Supplementary_files_format_and_content: For each Chip-Seq replicate, processed results are provided in the bed file.
|
| |
|
| Submission date |
Mar 17, 2019 |
| Last update date |
Jul 31, 2020 |
| Contact name |
Xiaoxiao Liu |
| E-mail(s) |
xxl244@case.edu
|
| Phone |
(216) 368-5293
|
| Organization name |
Case Western Reserve University
|
| Department |
Genetics and Genomes Sciences
|
| Lab |
Fulai Jin
|
| Street address |
10900 Euclid Ave
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44120 |
| Country |
USA |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE116825 |
Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases |
|
| Relations |
| BioSample |
SAMN11156922 |
| SRA |
SRX5532364 |
