|
| Status |
Public on Apr 20, 2019 |
| Title |
Mof_CreER_WT_rMof_D-3_4OHT_H4K16ac |
| Sample type |
SRA |
| |
|
| Source name |
Brown preadipocyte cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: BAT isolated brown preadipocytes
stage of adipogenesis: preadipocytes
chip antibody: anti-H4K16ac (Millipore, 07-329)
|
| Treatment protocol |
For culture, cells were plated in growth medium (DMEM plus 10% FBS) at a density of 1.8x106 cells per 15-cm dish 1~2 days before ChIP-seq.
|
| Growth protocol |
Primary brown preadipocytes were isolated from interscapular BAT of newborn Mof(flox/flox);CreER mice) and immortalized with SV40T-expressing retroviruses generated from the pBabeneo-large T plasmid
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq DNA sample prep kit (Cat no. FC-121-2001). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, 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 15-18 cycles and library fragments of 200-400 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 Genome Analyzer following the manufacturer's protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
Basecalls performed using Bcl2fastq
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2
Peaks were called using SICER with following configuration: For ChIP-seq of histone modifications: Windows (200), Gaps (200), FDR (1e-3);
Genome_build: mm9
Supplementary_files_format_and_content: wig files were generated using in-house script
|
| |
|
| Submission date |
Apr 19, 2019 |
| Last update date |
Apr 22, 2019 |
| Contact name |
Kai Ge |
| E-mail(s) |
kai.ge@nih.gov
|
| Phone |
301-451-1998
|
| Organization name |
NIH
|
| Department |
NIDDK
|
| Street address |
50 South Dr Rm 4154
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE130091 |
Selective binding of the PHD6 finger of MLL4 to histone H4K16ac links MLL4 and MOF |
|
| Relations |
| BioSample |
SAMN11467645 |
| SRA |
SRX5713556 |
