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Sample GSM3731762 Query DataSets for GSM3731762
Status Public on Apr 20, 2019
Title Mof_CreER_K274R_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 10 Center Dr Rm 8N307
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 SAMN11467650
SRA SRX5713551

Supplementary file Size Download File type/resource
GSM3731762_Mof_CreER_K274R_rMof_D-3_4OHT_H4K16ac_sorted-W200-G200-FDR1E-3-islandfiltered-normalized.wig.gz 1.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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