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Sample GSM2894549 Query DataSets for GSM2894549
Status Public on Mar 13, 2018
Title ChIP-seq_RAD21_WT
Sample type SRA
 
Source name HUES64
Organism Homo sapiens
Characteristics cell type: HUES64 human embryonic stem cells
chip antibody: RAD21 (abcam, ab992)
Growth protocol H9 human embryonic stem cells were obtained from WiCell. Cells were cultured in STEMPRO hESC SFM on cultureware coated with Geltrex Matrix at 37 °C under 5% CO2. Medium was changed every day. Cells were grown to 60-70% confluence before EdU labeling.
Extracted molecule genomic DNA
Extraction protocol Approximately 1x107 H9 hESCs were used to make each nasChIP-seq library. Anti-CTCF (Millipore) or -SMC1A (Millipore) antibodies were pre-incubated with Dynabeads Protein A beads (Thermo Fisher). Extracted chromatin was incubated with antibody-beads complex on a rotator at 4 °C for 5 hr. Beads were washed once with Wash Buffer (20 mM Tris-HCl pH 8.1, 500 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100, 0.1% SDS), twice with LiCl Buffer (10 mM Tris-HCl pH 8.1, 250 mM LiCl, 1 mM EDTA pH 8.0, 1% NP-40, 1% sodium deoxycholate), and once with 1x TE pH 8.0 with 50 mM NaCl. DNA was eluted by incubating beads in Elution Buffer at 65 °C for 30 min. Crosslinking-reversal, proteinase K digestion, phenol:chloroform:isoamyl alcohol extraction, ethanol precipitation, click chemistry, ethanol precipitation, streptavidin beads pull-down, and Illumina library preparation steps were the same as described above for nasBS-seq.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2500
 
Description processed file: HUES64_RAD21.bw
Data processing 50 bp paired-end reads were aligned to the human genome (hg38, XX) using bowtie2. Alignment score was controlled by applying bowtie2 option --score-min L,0,-0.4. Mapping uniqueness was controlled by selecting alignments with mapping quality Q>10 using Samtools. Peak calling and read density calculation were done using MACS2 (2.1.0) with BAMPE option (38). Matrix underlying heatmaps was generated with deepTools (2.5.4) (39) and was visualized using Java Treeview (40).
Genome_build: hg38
 
Submission date Dec 19, 2017
Last update date Mar 13, 2018
Contact name Chenhuan Xu
E-mail(s) chxu02@gmail.com
Organization name Beijing Institute of Genomics
Street address 1 Beichen West Road
City Beijing
ZIP/Postal code 100101
Country China
 
Platform ID GPL16791
Series (1)
GSE97394 Mapping DNA methylation and CTCF/cohesin occupancy on nascent chromatin and DNMT-targeted nascent chromatin
Relations
BioSample SAMN08203671
SRA SRX3482874

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

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