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Sample GSM1856005 Query DataSets for GSM1856005
Status Public on Jan 27, 2016
Title MNase-seq_control_Rep3
Sample type SRA
Source name MDA-MB-231
Organism Homo sapiens
Characteristics genotype/variation: Control cells (vector control)
passages: 3-7
antibody: N/A
Treatment protocol ChIP-Seq: Cells were lysed with Tris-HCl pH 8.0 based buffer with appropriate concentration of SDS. Chromatin fragmentation was performed by sonication with Bioruptor or Covaris. DNA was precipitated with antibody against each target protein.
MNase-seq: Cells were treated with a hypotonic buffer. Isolated nuclei were digested with MNase. DNA Mononucleosomal DNA was extracted by using a ZYMO RESEARCH cleanup column and QIAGEN Gel extraction kit.
ATAC-seq: Cells were treated with CSK buffer (10 mM PIPES pH 6.8, 100 mM NaCl, 300 mM sucrose, 3 mM MgCl2, 0.1% Triton X-100), and then chromatin tagmentation was performed by Tn5 transposase (5 µl in 25 µl total reaction, Nextera DNA Library Preparation Kit from Illumina).
Growth protocol Cells were grown on 15 cm plats in high glucose DMEM medium with 10% FBS
Extracted molecule genomic DNA
Extraction protocol Libraries were prepared according to Illumina or BIOO SCIENTIFIC instruction. ATAC-seq libraries were prepared by following the original protocol (Buenrostro et al., 2013) with several modifications (as described above)
Library strategy MNase-Seq
Library source genomic
Library selection MNase
Instrument model Illumina NextSeq 500
Description MNase-seq.Controlcells.Rep3.bigWig
Data processing Reads were filtered based on a mean base quality score >20. Reads were mapped to hg19 genome using Bowtie 0.12.8
For ATAC-seq data processing, we performed Trim Galore! to remove adapter sequence contamination. The offset parameters suggested by Buenrostro et al were applied to each mapped read.
Peak calling was performed with HOMER v4.1 at default parameters. Peaks were then adjusted to 200-mers centered on the midpoint of the HOMER calls.
Duplicate reads were removed using MarkDuplicates.jar from picard-tools-1.107 package.
All paired-end reads were converted to a single fragment. After normalization within each data set, bigWig files were generated to visualize the genomic coverage.
For RNA-seq data processing, read counts per gene per sample were collected by HTSeq-Count.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig, bed
Submission date Aug 18, 2015
Last update date May 15, 2019
Contact name Paul A Wade
Phone 919-541-3392
Organization name NIEHS
Department Laboratory of Molecular Carcinogenesis
Street address 111 TW Alexander Drive
City Research Triangle Park
State/province NC
ZIP/Postal code 27709
Country USA
Platform ID GPL18573
Series (1)
GSE72141 GATA3-mediated chromatin reprogramming in breast cancer cells
BioSample SAMN03998476
SRA SRX1156513

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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