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Sample GSM869207 Query DataSets for GSM869207
Status Public on Mar 07, 2012
Title input-BWA
Sample type SRA
Source name THP-1
Organism Homo sapiens
Characteristics cell line: THP-1
agent: None
sample pair: NA
chip antibody: none
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
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
BioSample SAMN02197677

Supplementary file Size Download File type/resource
GSM869207_s_7.bwa_hg19.n2.trunc35.mapq10.sorted_Input_DNA.bed.gz 47.5 Mb (ftp)(http) BED
Processed data provided as supplementary file
Raw data not provided for this record

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