|
| Status |
Public on Jan 01, 2022 |
| Title |
bone marrow cells 36N curcumin treatment |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow cells
|
| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: whole bone marrow cells
strain: C57BL/6
transgene: Nup98-HOXD13 transgenic
genotype: GFI1-36N
treatment: curcumin
chip antibody: H3K9ac(ab4441)
|
| Treatment protocol |
mice treated with or without curcumin 20mg/kg curcumin weekly by intraperitoneal (i.p.) injection
|
| Growth protocol |
Nup98-HOXD13 transgenic mice
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Trim Galore was used to remove adapters.
ChIP-seq reads were aligned to the mm10 genome assembly using BWA-MEM.
Low-quality reads were removed by Samtools. PCR duplicates were removed using Picard tool.
Peaks were called by MACS2 with default settings.
Peaks located within ENCODE black list regions were removed.
Genome_build: mm10
Supplementary_files_format_and_content: peak text files
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage
|
| |
|
| Submission date |
Dec 15, 2021 |
| Last update date |
Jan 02, 2022 |
| Contact name |
Xiaoqing Xie |
| E-mail(s) |
[email protected]
|
| Organization name |
Hematology, Oncology and Pneumology
|
| Department |
Department of Medicine A
|
| Street address |
Albert-Schweitzer-Campus 1
|
| City |
Muenster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE190974 |
Genome-wide maps of chromatin state in bone marrow cells |
|
| Relations |
| BioSample |
SAMN24088721 |
| SRA |
SRX13439469 |
