|
| Status |
Public on Mar 15, 2021 |
| Title |
MEL/ch11_HS3∆∆GA_H3K27ac_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
MEL/ch11
|
| Organism |
Mus musculus |
| Characteristics |
cell type: erythroleukemia cells
cell line: MEL/ch11
chip antibody: H3K27ac (Abcam, ab4729)
|
| Treatment protocol |
For transcriptional activation of the β-globin gene, MEL/ch11 cells were induced at a concentration of 1.5x10^5 cells/ml with 5 mM HMBA for 72 h.
|
| Growth protocol |
MEL/ch11 cells were cultured in DMEM medium containing 10% FBS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were digested with 100 units of MNase at 37°C for 15 min. Mono or di-nucleosomes sized chromatin was incubated with antibodies for 3 h at 4°C and recovered with protein A agarose beads.
ChIP DNA (10 ng for H3K27ac) was processed using NEBNext ChIP-seq library (New England Biolabs) with manufacturer’s instructions. The ends of ChIP DNA were repaired by NEBNext Ultra II End Prep enzyme mix and ligated with NEBNext adaptors. The concentration of adaptors was 1.5 µM for H3K27ac ChIP DNA. Adaptor-ligated DNA was selected at 200 bp size using NEBNext sample purification bead and amplified using the adaptor primers (7 cycles for H3K27ac). The fragments are purified using NEBNext sample purification beads. Final libraries were quantified with Qubit dsDNA HS assay (Invitrogen) and were sequenced single-end with a read length of 100 bp on an Illumina NovaSeq system.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
MEL/ch11 cells are murine erythroleukemia cells containing human chromosome 11.
|
| Data processing |
ChIP-seq raw reads were trimmed to 36 bp using trim sequences tool. Trimmed reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to the hg19 canonical genome using Bowtie2. Aligned BAM files were filtered by Minimum MAPQ quality score 20 and sorted by chromosomal coordinates. Potential PCR duplicates were removed from BAM files. Peak regions were identified using MACS2 providing input chromatin data as control.
Genome_build: hg19 chromosome11
Supplementary_files_format_and_content: bigwig
|
| |
|
| Submission date |
Mar 16, 2020 |
| Last update date |
Mar 16, 2021 |
| Contact name |
AeRi Kim |
| E-mail(s) |
kang3000j@pusan.ac.kr
|
| Organization name |
Pusan national university
|
| Street address |
2, Busandaehak-ro 63beon-gil, Geumjeong-gu
|
| City |
Busan |
| ZIP/Postal code |
46241 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE147037 |
Histone H3K27 acetylation at CTCF sites mediates cell type-specific chromatin interactions between them |
|
| Relations |
| BioSample |
SAMN14382704 |
| SRA |
SRX7916255 |
