 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 07, 2012 |
| Title |
THP1-LPS-1-BWA-H3K9/K14Ac |
| Sample type |
SRA |
| |
|
| Source name |
THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
agent: LPS
sample pair: 1
chip antibody: H3K9/K14Ac
|
| Treatment protocol |
THP-1 macrophages were then either left unstimulated (control) or stimulated with 1ug/ml LPS (LPS-stimulated) from Escherichia coli O55:B5 for 2 hours (Sigma Chemical Co., St. Louis, MO, USA) to induce an acute inflammatory response. To confirm an induction of the inflammatory response in the THP-1 macrophages, TNF mRNA levels were measured in control and LPS-stimulated samples.
|
| Growth protocol |
THP-1 cells (monocyte cell line) (ATCC , Manassas, VA, USA) were maintained in culture in RPMI 1640 medium containing 10% fetal bovine serum, 1mM sodium pyruvate , 100 units/ml penicillin and 100 μg/ml streptomycin at 37°C with 5% CO2. For differentiation of THP-1 cells into macrophages a protocol using conditioned media as previously described by Whatling et al was used. To confirm differentiation of THP-1 monocytes into macrophages CD11b expression was measured using FACS and quantitative polymerase chain reaction (qPCR).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA-protein complexes were eluted, treated with RNaseA (USB,Cleveland, OH, USA) for 4-6 hours at 45°C and Proteinase K (USB, Cleveland, OH, USA) overnight at 65°C. DNA was extracted by phenol/chloroform/isoamyl alcohol extraction, purified and resuspended in water. library construction: Illumina core center, standard protocol
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
| |
|
| Data processing |
Sequence reads were 35 bases or longer but truncated to 35 bases to ensure base quality over the entire read. Reads were aligned to the human reference genome (GRCh37/hg19) with Burrows-Wheeler Alignment tool (BWA) (Li H and Durbinv R (2009) Fast and accurate short read alignment with Burrows-Wheeler transform.
|
| |
|
| Submission date |
Feb 01, 2012 |
| Last update date |
Jun 11, 2013 |
| Contact name |
Lasse Folkersen |
| E-mail(s) |
lwf@ngc.dk
|
| Organization name |
National Genome Center
|
| Department |
Bioinformatics
|
| Street address |
Artellerivej
|
| City |
Copenhagen |
| ZIP/Postal code |
2300 |
| Country |
Denmark |
| |
|
| Platform ID |
GPL9052 |
| Series (2) |
| GSE32324 |
ChIP-seq analysis LPS stimulated THP-1 cells |
| GSE32325 |
Expression and ChIP-seq analysis LPS stimulated THP-1 cells |
|
| Relations |
| BioSample |
SAMN02197674 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM869204_s_2.bwa_hg19.n2.trunc35.mapq10.sorted_LPS_A.bed.gz |
15.3 Mb |
(ftp)(http) |
BED |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
|
|
|
|
 |
