|
| Status |
Public on Dec 01, 2011 |
| Title |
Control_ChIPseq |
| Sample type |
SRA |
| |
|
| Source name |
THP-1, control ChIP-Seq
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
cell type: monocytic cells
treatment 1: differentiation with PMA (50ng/ml;40hrs)
treatment 2: 1.5 h of 1microM Rosiglitazone
chip antibody: normal mouse IgG
antibody vendor: Santa Cruz
antibody catalog #: sc-2025
antibody lot #: H0709
|
| Treatment protocol |
THP-1 cells were differentiated with 50ng/ml of PMA for 40hrs, followed by treatment with Rosiglitazone for 1.5 hrs.
|
| Growth protocol |
THP-1 cells were passaged in suspension prior to treatment; RPMI medium, 10%FBS, Pen/Strep.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using phenol/chloroform extraction followed by ethanol precipitation.
10ng of DNA as per manufacturer's protocol. Briefly, using the Solexa ChIP-Seq DNA sample preparation kit, universal linkers were added to the chromatin fragments and DNA was PCR amplified for 15 cycles. DNA was gel-purified and fragments between 200-300bp were selected for sequencing.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Description |
Chromatin IP using IgG.
|
| Data processing |
The raw images have been processed using the Solexa Pipeline and were mapped to the reference genome (NCBI36/hg18) using Eland software with maximal two-mismatches.
Peak detection was performed using CCAT (Xu et al. 2010). Regions enriched in the specific libraries were tested for significance against the tag distribution in a control library (IgG). Peaks with FDR <0.01 were considered for analysis.
|
| |
|
| Submission date |
Nov 16, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Sebastian Pott |
| E-mail(s) |
spott@uchicago.edu
|
| Organization name |
University of Chicago
|
| Department |
Human Genetics
|
| Street address |
920 58th Street
|
| City |
Chicago |
| State/province |
Il |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE25426 |
Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages: human ChIP-Seq |
| GSE25608 |
Functional and cellular constraints that shaped the PPARg binding landscape in human and mouse macrophages |
|
| Relations |
| SRA |
SRX103225 |
| BioSample |
SAMN00744393 |
