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Sample GSM2587055 Query DataSets for GSM2587055
Status Public on Sep 28, 2017
Title THP-1, GABPA 24 h EtOH
Sample type SRA
 
Source name human monocytic cell line THP-1
Organism Homo sapiens
Characteristics cell line: THP-1
cell type: monocytic leukemia cells
chip antibody: GABP-a (Santa Cruz sc-28312 X)
treatment protocol: 24 h EtOH
Treatment protocol Treated with EtOH or 24 h 100 nM 1,25(OH)2D3
Growth protocol THP-1 human monocytic leukemia cells were grown in RPMI 1640 supplemented with 10% fetal calf serum, 2 mM L-glutamine, 0.1 mg/ml streptomycin and 100 U/ml penicillin and the cells were kept at 37 °C in a humidified 95% air/ 5% CO2 incubator.
Extracted molecule genomic DNA
Extraction protocol Proteins were crosslinked with formaldehyde to DNA, then GABPA-bound fragments were pulled down by chromatin immunoprecipitation
ChIP-seq library was prepared from 5-10 ng ChIP DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) per manufacturer's protocol
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description Chromatin IP against GABPA
Data processing Alignment to hg19 using Bowtie v1.0 parameters: -n 1 – k 1 -m 1 -l 32 -t -q –best
Peak discovery using MACS2 parameters: -m 5 50 –bw 150
Genome_build: hg19
Supplementary_files_format_and_content: tdf
 
Submission date Apr 24, 2017
Last update date May 15, 2019
Contact name Carsten Carlberg
E-mail(s) carsten.carlberg@uef.fi
Organization name University of Eastern Finland
Department Institute of Biomedicine
Street address Yliopistonranta 1D
City Kuopio
ZIP/Postal code 70211
Country Finland
 
Platform ID GPL11154
Series (1)
GSE98093 GABPA ChIP-seq in human monocytic THP-1 cells
Relations
BioSample SAMN06821055
SRA SRX2754626

Supplementary file Size Download File type/resource
GSM2587055_THP1_GABPA_E.tdf 237.1 Mb (ftp)(http) TDF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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