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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
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
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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