|
| Status |
Public on Jan 03, 2022 |
| Title |
M11_dC5-7 H3K27me3_ChIP-Seq |
| Sample type |
SRA |
| |
|
| Source name |
MEL/ch11
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MEL/ch11
cell type: erythroleukemia cells
genotype/variation: C5-, C6- and C7-deleted (dC5-7)
chip antibody: H3K27me3 (Millipore, 07-449)
|
| 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 and 1 ng for H3K27me3) was processed using NEBNext Ultra II DNA Library Prep Kit (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. Adaptor-ligated DNA was selected at 175-200 bp size using NEBNext sample purification bead and amplified using the adaptor primers (7 cycles for H3K27ac and 10-11 cycles for H3K27me3). The fragments are purified using NEBNext sample purification beads.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
ChIP-seq raw reads were filtered to remove input read ends with poor quality values (quality score 20) and then aligned to the human chromosome 11 (hg19 genome assembly) 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. Bigwig files generated from BAM files using BamCoverage. ChIP-seq signals were normalized by S3V2-IDEAS method.
Genome_build: Human chromosome 11 (hg19, GRCh37)
Supplementary_files_format_and_content: bigWig
|
| |
|
| Submission date |
Jan 05, 2021 |
| Last update date |
Jan 03, 2022 |
| 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) |
| GSE164288 |
Multiple CTCF sites contribute to stable enhancer-promoter interactions in the β-globin locus |
|
| Relations |
| BioSample |
SAMN17217636 |
| SRA |
SRX9785559 |
