|
| Status |
Public on May 20, 2010 |
| Title |
3T3-L1_0hr_H3K9ac |
| Sample type |
SRA |
| |
|
| Source name |
Chromatin IP against acetylated H3 lysine 9
|
| Organism |
Mus musculus |
| Characteristics |
cell line: 3T3-L1
developmental stage: undifferentiated
chip antibody: H3K9ac (Upstate Biotechnologies, 06-942)
|
| Treatment protocol |
ChIP was performed as described using cross-linked 3T3-L1 nuclear lysates.
|
| Growth protocol |
3T3-L1 cells were obtained from American Type Culture Collection and differentiated to adipocytes according to standard protocol. All cells were cultured in high-glucose DMEM supplemented with 10% fetal bovine serum and 100 U/ml penicillin and 100 μg/ml streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP samples were amplified using the ChIP-Seq Sample Prep Kit (Illumina) according to manufacturer's instructions. Sequence reads of 36 bp were obtained using the Solexa Analysis Pipeline, and mapped to the mouse genome (mm8) using ELAND allowing up to two mismatches. Uniquely positioned reads were included for further analysis such that each start coordinate was represented once.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Description |
Peak file reports regions outside of TSS and differentially enriched for H3K9ac at 0 hr relative to 24 or 240 hr of differentiation
|
| Data processing |
Peak detection for H3K9ac ChIPseq data was determined by STAR. CEBPb and GR transcription factor binding data were analyzed with GLITR. Masking file contains regions enriched in input DNA from 3T3-L1 cells.
Input sample: GSM544723: 3T3-L1_0hr_Input
|
| |
|
| Submission date |
May 19, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
David Steger |
| E-mail(s) |
stegerdj@mail.med.upenn.edu
|
| Organization name |
University of Pennsylvania
|
| Street address |
415 Curie Blvd
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL9250 |
| Series (1) |
| GSE21898 |
Propagation of Adipogenic Signals through an Epigenomic Transition State |
|
| Relations |
| SRA |
SRX020949 |
| BioSample |
SAMN00013665 |
