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| Status |
Public on Aug 21, 2024 |
| Title |
CTCF_CTCFAID_ESC_auxin2d_2 |
| Sample type |
SRA |
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| Source name |
CTCF_degron_auxin_treated_ESCs
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| Organism |
Mus musculus |
| Characteristics |
cell type: Embryonic stem cells
genotype: CTCF_degron_auxin_treated
cell line: E14
chip antibody: CTCF (Millipore, #07-729)
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| Growth protocol |
mESCs were cultured in standard medium supplemented with LIF and 2i conditions (1 mM MEK1/2 inhibitor (PD0325901, Stemgent) and 3 mM GSK3 inhibitor (CHIR99021, Stemgent)).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed as described in Oksuz et al., 2018 using buffers in the following order: LB1 (50 mM HEPES, pH 7.5 at 4 C, 140 mM NaCl, 1 mM EDTA, 10% Glycerol, 0.5% NP40, 0.25% Triton X) for 10 min at 4 C, LB2 (10 mM Tris, pH 8 at 4 C, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA) for 10 min at RT, and LB3 (10 mM Tris, pH 7.5 at 4 C, 1 mM EDTA, 0.5 mM EGTA, and 0.5% N-Lauroylsarcosine sodium salt). Chromatin was sonicated to an average size of ~250 bp using a Diagenode Bioruptor. ChIP was performed by using antibodies listed. Chromatin fromDrosophila(1:100 ratio to ESC or MN derived chromatin), andDrosophila-specific H2Av antibody were used as spike-in control in each sample.
Libraries were prepared according to manufacturer’s instructions (Illumina) as described in Narendra et al., 2015. Immunoprecipitated DNA was first end-repaired using End-It Repair Kit (Epicenter), tailed with an A using Klenow exo minus (NEB M0212), ligated to custom adapters, and fragments of 300±100 bp were size-selected. These fragments were amplified through ligation-mediated PCR amplification (LM-PCR) by using Q5 polymerase (NEB M0530).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequence reads were mapped to mm10 reference genome with Bowtie 2.
After normalization with the spike-in Drosophila read counts for all (except for normalization with total counts for RAD21), normalized ChIP-seq read densities were visualized in Easeq Software and/or Integrative Genomics Viewer (IGV).
Assembly: mm10
Supplementary files format and content: bigwig
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| Submission date |
Apr 24, 2023 |
| Last update date |
Aug 21, 2024 |
| Contact name |
Danny Reinberg |
| Organization name |
University of Miami
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| Department |
Sylvester Cancer Center/Human Genetics
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| Lab |
Reinberg Lab
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| Street address |
1501 NW 10th Ave
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| City |
Miami |
| State/province |
Florida |
| ZIP/Postal code |
33136 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE230481 |
Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries [ChIP-Seq2] |
| GSE230482 |
Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries |
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| Relations |
| BioSample |
SAMN34356291 |
| SRA |
SRX20088479 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7225042_CTCF_CTCFAID_ESC_auxin2d_2.bw |
35.1 Mb |
(ftp)(http) |
BW |
| GSM7225042_HOK_4_narrow_peaks.narrowPeak.gz |
47.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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