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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Mar 24, 2017 |
| Title |
ChIP-Seq-delA-L1-GR-rep1 |
| Sample type |
SRA |
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| Source name |
delA-L1-GR
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Mammary gland
state: day one of lactation
genotype: CTCF-delA
chip antibody: GR (Thermo Scientific, PA1-511A)
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| Treatment protocol |
Frozen-stored mammary tissues collected at lactation day 1 (L1) were ground into powder. Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then was quenched with glycine (0.125 M final concentration). Samples were processed as previously described (27). The following antibodies were used for ChIP-seq: CTCF (Millipore, 07-729 and Abcam, ab70303), SMC1 (Bethyl, A300-055A), STAT5A (Santa Cruz Biotechnology, sc-1081), GR (Thermo Scientific, PA1-511A), H3K27ac (Abcam, ab4729) and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 2500 instrument (Illumina).
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| Growth protocol |
All animals were bred along the guidelines of the NIH and all animal experiments were performed according to the Animal Care and Use Committee (ACUC) of the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK). The CRISPR/Cas9 system was used to generate mutant mice with CTCF binding site deletions from C57BL/6 mice (Charles River) by the transgenic core of the National Heart, Lung, and Blood Institute (NHLBI). Single-guide RNA (sgRNA) constructs were designed to specifically target the individual CTCF binding sites in the casein (Csn) locus (http://crispr.mit.edu/). Target-specific sgRNA and Cas9 mRNA were in vitro transcribed and microinjected into the cytoplasm of fertilized eggs for founder mouse production. To screen homozygous mice, all mice were genotyped by PCR amplification with genomic DNA from mouse tail and sequencing (Macrogen).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries for sequencing were prepared using standard Illumina protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
ChIP-seq signals were trimmed using trimmomatic (Bolger et al., Bioinformatics, 2014) to filter low-quality reads and subsequently aligned to the mouse reference genome (mm10) using Bowtie aligner (Langmead et al., Nature methods, 2012) with the -m 1 parameter to obtain only uniquely mapped reads, except for CTCF samples where the -m 3 and --best parameters were used. HOMER software (Heinz et al., Mol. Cell, 2010) was applied for visualization.
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph
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| Submission date |
Dec 19, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Michaela Willi |
| Organization name |
NIH
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| Department |
NIDDK
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| Street address |
9000 Rockville Pike
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| City |
Bethesda |
| ZIP/Postal code |
20814 |
| Country |
USA |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE92591 |
Functional analysis of CTCF sites associated with cytokine-sensing mammary-specific enhancers in the complex casein locus [ChIP-seq] |
| GSE95758 |
Functional analysis of CTCF sites associated with cytokine-sensing mammary-specific enhancers in the complex casein locus |
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| Relations |
| BioSample |
SAMN06165930 |
| SRA |
SRX2436115 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2433087_ChIP-Seq-delA-L1-GR-rep1.ucsc.bedGraph.gz |
64.5 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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