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| Status |
Public on Aug 31, 2015 |
| Title |
ChIPSeq_WT_EZH1_rep2 |
| Sample type |
SRA |
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| Source name |
Mammary gland
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| Organism |
Mus musculus |
| Characteristics |
strain: Mixed C57BL/6 x FVB/N
tissue: Mammary gland
state: pregnancy day of 13
genotype: wild type
chip antibody: EZH1 (a generous gift from Dr. Sartorelli)
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| Growth protocol |
We mated Ezh2f/f mice (Ezhkova et al., 2011; Wang et al., 2010) with the control transgenic mouse line A (Wagner et al., 1997) in order to generate mice with mammary-specific deletion of Ezh2. Ezh1 knockout mice were obtained from Rockefeller University (Ezhkova et al., 2011). Genotyping was confirmed by PCR using DNAs from ear clips. All animals were handled and housed in accordance with the guidelines of the National Institutes of Diabetes, Digestive and Kidney Diseses Animal Care and Use Committee.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen-stored mammary tissues from p13 were broken into powder with mortar and pestle. Nuclei were extracted in Farnham lysis buffer (5mM PIPES PH8.0, 85mM KCl, 0.5% NP-40 and protease inhibitor). Antibodies against EZH1 (gift from Sartorelli, Mousavi et al. Mol. Cell 2012), EZH2 (Diagenode, cat# C15410039 and lot# 003), STAT5 (Santa Cruz Biotechnology, cat# sc-1081; L-20, lot# L2012, 10ug) H3K27me3 (Millipore, 07-449) and PolII (Abcam, cat# ab5408, lot# GR106949-6) were used for ChIP.
Libraries were prepared for sequencing using standard Illumina protocols.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Basecalls performed using the CASAVA software
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie2 program (Langmead et al., Nature method, 2012)
processed data files format and content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Genome_build: mm9
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| Submission date |
Jul 01, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Sumin Oh |
| E-mail(s) |
sumin.oh@nih.gov
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| Phone |
301-496-8727
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| Organization name |
NIH
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| Department |
NIDDK
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| Lab |
LGP
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| Street address |
9000 Rockville Pkie
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| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE70440 |
Loss of EZH2 results in precocious mammary gland development and the activation of STAT5-dependent genes |
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| Relations |
| BioSample |
SAMN03835538 |
| SRA |
SRX1078985 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1754901_ChIPSeq_WT_EZH1_rep2.ucsc.bedGraph.gz |
77.2 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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