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| Status |
Public on Jun 04, 2020 |
| Title |
ChIP-seq-WT-L1-H3K4me3-rep1 |
| Sample type |
SRA |
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| Source name |
Mammary gland
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| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: wild-type
Stage: Lactation day 1
tissue: Mammary gland
chip-antibody: H3K4me3 (Millipore, 17-614)
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| Growth protocol |
Mouse mammary tissues were harvested at day one of lactation (L1), and day 6 and day 18 of pregnancy (p6 and p18).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Mammary tissues from specific stages during pregnancy and lactation were harvested, and stored at -80°C. The frozen-stored tissues were ground into powder in liquid nitrogen. Chromatin was fixed with formaldehyde (1% final concentration) for 15 min at room temperature, and then quenched with glycine (0.125 M final concentration). Samples were processed as previously described. The following antibodies were used for ChIP-seq: STAT5A (Santa Cruz Biotechnology, sc-1081), GR (Thermo Fisher Scientific, PA1-511A), H3K27ac (Abcam, ab4729), H3K4me3 (Millipore, 17-614), NFIB (Santa Cruz Biotechnology, sc-5567), and RNA polymerase II (Abcam, ab5408). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 2500 instrument (Illumina).
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 |
The ChIP-seq analysis workflow comprised trimming using trimmomatic (Bolger et al., Bioinformatics, 2014) in order to filter low quality reads, followed by the application of bowtie aligner (Langmead et al., Nature methods, 2012) with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools (Broad Institute. Picard, http://broadinstitute.github.io/picard/.) to remove duplicates. Deeptools (Ramírez et al., Nucleic Acids Research, 2016) was applied for the generation of bedGraph files.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: bedGraph of ChIP-seq.
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| Submission date |
Feb 25, 2019 |
| Last update date |
Jun 04, 2020 |
| 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) |
| GSE127139 |
Cytokine-sensing primary enhancer cluster launches secondary enhancers to activate multi-gene locus [ChIP-seq] |
| GSE127144 |
Cytokine-sensing primary enhancer cluster launches secondary enhancers to activate multi-gene locus |
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| Relations |
| BioSample |
SAMN11014086 |
| SRA |
SRX5426652 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3629404_ChIP-seq-WT-L1-H3K4me3-rep1.bedGraph.gz |
480.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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