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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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