|
| Status |
Public on Feb 01, 2013 |
| Title |
Input for H3K4me3 and H3K27me3 |
| Sample type |
SRA |
| |
|
| Source name |
3T3-L1 preadipocytes
|
| Organism |
Mus musculus |
| Characteristics |
strain: mixed C57/BL6-129
cell type: 3T3-L1 preadipocytes
antibody: none
|
| Treatment protocol |
adipogenesis inducing cocktails
|
| Growth protocol |
3T3-L1 preadipocytes were routinely cultured in DMEM plus 10% BS.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody. For ChIP antibodies, Anti-H3K9me2 antibody from Millipore (17-648) was used for ChIP and ChIP-Seq; for H3K27me3, Millipore (07-499); for H3K4me3, Millipore 07-473. ChIP was performed by following a protocol from R. Myers’ lab (http://www.hudsonalpha.org/myers-lab/protocols). The sequencing libraries were constructed with ChIP-Seq DNA Sample Prep kit (Illumina) and were sequenced on Illumina HiSeq 2000 system. The ChIP-enriched regions were identified using SICER (Zang et al, 2009), an algorithm designed to capture domains of diffuse signals.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample5
|
| Data processing |
Base-calling and alignment performed by Illumina Analysis Pipeline
Conversion to BED format by bed tools v2.16
Genome_build: NCBI37 (mm9)
Supplementary_files_format_and_content: bed format containing the genomic coordinates of each mapped read
|
| |
|
| Submission date |
Oct 10, 2012 |
| Last update date |
May 15, 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 |
GPL13112 |
| Series (2) |
| GSE41455 |
Histone H3K9 Methyltransferase G9a Represses PPARγ Expression and Adipogenesis [ChIP-Seq and RNA-Seq data] |
| GSE41457 |
Histone H3K9 Methyltransferase G9a Represses PPARγ Expression and Adipogenesis |
|
| Relations |
| SRA |
SRX193356 |
| BioSample |
SAMN01760773 |
