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| Status |
Public on May 31, 2016 |
| Title |
ChIPSeq_Wap-delE3_L1_STAT5A_rep2 |
| Sample type |
SRA |
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| Source name |
Mammary
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| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Mammary gland
state: lactation day 1
genotype: Wap-delE3
chip antibody: STAT5A (Santa Cruz, sc-1081)
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| Growth protocol |
C57BL/6 mice were purchased from Charles River. Wap-delE1a, -delE1b, -delE1c, -delE2, -delE3, -delE1a_delE2, -delE2_delE3 and -delE1a_delE2_delE3 were inter-bred to maintain homozygosity. Genotyping was confirmed by PCR followed by the DNA sequencing using genomic DNAs from a tail snip. All animals were handled and housed in accordance with the guidelines of the National Institute of Diabetes, Digestive and Kidney Diseases Animal Care and Use Committee.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Frozen-stored mammary tissues from L1 and 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 inhibitors). Mammary epithelial cells were isolated from fresh L1 and p13 mammary tissues. Antibodies against STAT5A (Santa Cruz, sc-1081), GR (Thermo Scientific, PA1-511A), MED1 (Bethyl laboratory, A300-793A), H3K27ac (Abcam, Ab4729), NFIB (Santa Cruz, sc-5567), ELF5 (Santa Cruz, sc-9645), RNA Pol II (Abcam, Ab5408) and H3K4me3 (Milllipore, 17-614) 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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| Description |
ChIP-seq
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| Data processing |
ChIP-seq reads were aligned to the mm9 genome assembly using the Bowtie aligner (Langmead et al., Nature method, 2012)
DNase-seq reads were aligned to the mm9 genome assembly using the Bowtie aligner (Langmead et al., Nature method, 2012)
Genome_build: mm9
Supplementary_files_format_and_content: ChIP-seq: BedGraph files can be used to check ChIP-seq peaks through the UCSC genome browser.
Supplementary_files_format_and_content: DNase-seq: BedGraph files can be used to check DNase-seq peaks through the UCSC genome browser.
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| Submission date |
Mar 31, 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 |
GPL13112 |
| Series (1) |
| GSE74826 |
Hierarchy within the mammary STAT5-driven Wap super-enhancer |
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| Relations |
| BioSample |
SAMN04594995 |
| SRA |
SRX1672056 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2102951_ChIPSeq_WT_Wap-delE3_STAT5A_rep2.ucsc.bedGraph.gz |
71.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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