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Sample GSM1057021 Query DataSets for GSM1057021
Status Public on Sep 20, 2013
Title H3K27Ac_ChIPSeq_rep2_B
Sample type SRA
 
Source name Peripheral blood cells
Organism Homo sapiens
Characteristics cell type: CD14+ monocytes
chip antibody: H3K27ac (Abcam ab-4729)
experimental condition: Cultured with MCSF (10ng/ml) and IFN-gamma (100U/ml) for 24 hours.
Treatment protocol Cells were treated with or without IFN-g (100U/ml) for 24 hours, and then stimulated with LPS (50ng/ml) for 3 or 6 hours as indicated.
Growth protocol Peripheral blood mononuclear cells were obtained from the blood of healthy donors by density gradient centrifugation using Ficoll (Invitrogen) and a protocol approved by the Hospital for Special Surgery Institutional Review Board. CD14+ human monocytes were purified from PBMCs by positive selection using anti-CD14 magnetic beads as recommended by the manufacturer (Miltenyi Biotec). Monocytes were cultured in Roswell Park Memorial Institute (RPMI) 1640 medium (Invitrogen) supplemented with 10% heat-inactivated defined FBS (HyClone), penicillin/streptomycin (Invitrogen), L-glutamine (Invitrogen), and 10 ng/mL human macrophage colony-stimulating factor (M-CSF; Peprotech).
Extracted molecule genomic DNA
Extraction protocol Sonicated cell lysates of nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, Klenow polymerase and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (3’ to 5’ exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was purified using MinElute PCR Purification kit and PCR amplified with Illumina primers for 15 cycles. Library fragments of 200-300 bp were band isolated from an 1.5% agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina HiSeq 2000 Sequencer following the manufacturer's protocols.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Data processing Basecalls performed using CASAVA version 1.7
ChIP-seq reads were aligned to the hg19 genome assembly using BOWTIE with default configurations.
peaks were called using ChIPSeeqer with the following setting: STAT1 -t_15 -t_fold 2; H3K27Ac -t_20 -t_fold 3 ; IRF1 -t_15 -t_fold 2;
Genome_build: hg19
Supplementary_files_format_and_content: wig files were generated using ChIPSeeqer

The headers for peak *txt files are as follows (from the left):

Chromosome : chromosome name
Start_Position : the first (genomic) coordinate of the peak
End_Position : the second (genomic) coordinate of the peak
Avg_p-value : average log p-value of the nucleotides in the normalized peak region
Score : score estimated as the average ChIP reads/length of peak (minus the average INPUT reads/length of peak - if INPUT is available)
Posmaxpeakheight : the position of the maximum height of the peak
Maxpeakheight : the maximum peak height (in reads)
RelPosMaxPeakHeight(%) : the relative position of the maximum height of the peak, e.g., 50% means the highest point is at the middle of the peak
Peak_Size : the size of the peak (in bp)
Mid_point : the middle position of the peak
Summit_dist_from_mid : the distance of the maximum height from the middle of the peak
 
Submission date Dec 21, 2012
Last update date May 15, 2019
Contact name Lionel Ivashkiv
Organization name Hospital for Special Surgery
Street address 535 East 70th Street
City New York
State/province NY
ZIP/Postal code 10021
Country USA
 
Platform ID GPL11154
Series (1)
GSE43036 Synergistic Activation of Inflammatory Cytokine Genes by Priming of Regulatory DNA Elements for Increased Transcription in Response to TLR Signaling
Relations
SRA SRX212658
BioSample SAMN01874817

Supplementary file Size Download File type/resource
GSM1057021_H3K27Ac_B2.wig.gz 459.8 Mb (ftp)(http) WIG
GSM1057021_H3K27acPeak_B2.txt.gz 2.0 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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