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Status |
Public on Mar 07, 2012 |
Title |
input |
Sample type |
SRA |
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Source name |
THP-1
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Organism |
Homo sapiens |
Characteristics |
cell line: THP-1 agent: none sample pair: NA chip antibody: none
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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.
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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).
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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
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina Genome Analyzer |
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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. Bioinformatics 25 (14): 1754-60), and only uniquely mapped reads with a maximum of 2 mismatched bases were considered for further analysis. The sequence tag density generated from the input library (total DNA) was used as background.
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Submission date |
Sep 23, 2011 |
Last update date |
Jun 11, 2013 |
Contact name |
Lasse Folkersen |
E-mail(s) |
lwf@ngc.dk
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Organization name |
National Genome Center
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Department |
Bioinformatics
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Street address |
Artellerivej
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City |
Copenhagen |
ZIP/Postal code |
2300 |
Country |
Denmark |
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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 |
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Relations |
BioSample |
SAMN02198036 |
Supplementary file |
Size |
Download |
File type/resource |
GSM800790_s_7.hg19.n2.mapqual1.aln.bed.gz |
53.9 Mb |
(ftp)(http) |
BED |
Processed data provided as supplementary file |
Raw data not provided for this record |
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