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Sample GSM1659606 Query DataSets for GSM1659606
Status Public on Apr 30, 2019
Title MEL_PU.1_D5R2
Sample type SRA
Source name MEL
Organism Mus musculus
Characteristics cell type: MEL
chip antibody: PU.1
time: D5
Growth protocol Mouse erythroleukemia cells (MEL, ATCC, Manassas, VA) were grown in RPMI-1640 medium (Life Technologies, Carlsbad, CA) supplemented with penicillin/streptomycin (Life Technologies) and 10% FBS (VWR, Radnor, PA). MELs grown to a density of 1 million/ml were differentiated using 2% DMSO (VWR) added to the medium and the cells were grown for another 5 days to induce the expression of hemoglobin genes. At least 80-90% of cells expressed hemoglobin based on their color and benzidine/hydrogen peroxide staining result. Trypan Blue (VWR) staining was performed before harvesting the cells for each assay in order to make sure that at least 90% of the cells were viable. All experiments were done with 2 biological replicates.
Extracted molecule genomic DNA
Extraction protocol Samples were extracted accoding to the Myers Lab ChIP-seq protocol v042211 (
MEL PU.1 ChIP-seq libraries was made based on Myers Lab protocol v042211 ( using a rabbit polyclonal IgG PU.1 antibody (Santa Cruz Technology, sc-352, Lot#B0513, 200μg/ml). The quality of ChIP was validated by qPCR through the use of primers flanking known PU.1 binding sites (ex. SPI1, FCGR28, NRIH3) and known negative control sites (ex. MYOD1, ACTA1). The best two undifferentiated and differentiated MEL PU.1 ChIP replicates were constructed into Illumina sequencing libraries.
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
Data processing PU.1 ChIP-seq reads were aligned to the mouse genome (mm9) with bowtie version 1.0.0 (Langmead et al. 2009) using the following settings: -S, –k 10, -m 10, --best, and --strata.
Peaks were called from the alignments using MACS2 version 2.0.10 (options: -p1e-3, -f BAM), and reproducible peaks were determined between the replicates using the Irreproducible Discovery Rate (IDR)(Li et al. 2011)
Reproducible replicate peaks that had IDRs < 0.05 and that were not present within mouse genomic blacklisted regions were used for downstream analyses.
Genome_build: mm9
Supplementary_files_format_and_content: Provided are 1) the unfiltered MACS2 peaks for each MEL PU.1 ChIP-seq replicate at day 0 (undifferentiated) and day 5 (differentiated with DMSO) in bed format (macs2_MEL_PU.1_d0r1_peaks.encodePeak, macs2_MEL_PU.1_d0r2_peaks.encodePeak, macs2_MEL_PU.1_d5r1_peaks.encodePeak, macs2_MEL_PU.1_d5r2_peaks.encodePeak), and 2) the IDR reproducible peaks between replicate sets that are filtered of blacklisted regions (MEL.PU1.peaks.d0.idrmerged.NOBLKlist.bed, MEL.PU1.peaks.d5.idrmerged.NOBLKlist.bed)
Submission date Apr 16, 2015
Last update date May 15, 2019
Contact name Marissa Macchietto
Organization name University of Minnesota, Minneapolis
Department Minnesota Supercomputing Institute
Street address 117 Pleasant Street SE
City Minneapolis
ZIP/Postal code 55455
Country USA
Platform ID GPL13112
Series (1)
GSE67955 The landscape of global-long range interactions in mouse and human blood cell lines mediated by Yy1, GATA1, and CTCF during differentiation
BioSample SAMN03487305
SRA SRX997431

Supplementary file Size Download File type/resource
GSM1659606_macs2_MEL_PU.1_d5r2_peaks.encodePeak.txt.gz 349.6 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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