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Status |
Public on Mar 13, 2018 |
Title |
ChIP-seq_RAD21_WT |
Sample type |
SRA |
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Source name |
HUES64
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Organism |
Homo sapiens |
Characteristics |
cell type: HUES64 human embryonic stem cells chip antibody: RAD21 (abcam, ab992)
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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.
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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.
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2500 |
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Description |
processed file: HUES64_RAD21.bw
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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
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Submission date |
Dec 19, 2017 |
Last update date |
Mar 13, 2018 |
Contact name |
Chenhuan Xu |
E-mail(s) |
chxu02@gmail.com
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Organization name |
Beijing Institute of Genomics
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Street address |
1 Beichen West Road
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City |
Beijing |
ZIP/Postal code |
100101 |
Country |
China |
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Platform ID |
GPL16791 |
Series (1) |
GSE97394 |
Mapping DNA methylation and CTCF/cohesin occupancy on nascent chromatin and DNMT-targeted nascent chromatin |
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Relations |
BioSample |
SAMN08203671 |
SRA |
SRX3482874 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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