 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 18, 2018 |
| Title |
ChIP-seq-delE1-delE3-L1-GR_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6
genotype/variation: Wap-delE1-delE3
Stage: Lactation day 1
tissue: Mammary gland
chip antibody: GR (Thermo Scientific, PA1-511A)
|
| Growth protocol |
Mouse mammary and kidney tissues were harvested at day one and ten of lactation (L1 and L10).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Libraries for sequencing were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| 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. Homer software (Heinz et al., Mol. Cell, 2010) was applied for the generation of bedGraph files.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *bedGraph: bedGraph of ChIP-seq.
|
| |
|
| Submission date |
Jun 05, 2018 |
| Last update date |
Sep 21, 2018 |
| Contact name |
Michaela Willi |
| Organization name |
NIH
|
| Department |
NIDDK
|
| Street address |
9000 Rockville Pike
|
| City |
Bethesda |
| ZIP/Postal code |
20814 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE115368 |
Progressing enhancer landscape during mammary differentiation controls gene regulation [ChIP-seq] |
| GSE115370 |
Progressing super-enhancer landscape during mammary differentiation controls tissue-specific gene regulation |
|
| Relations |
| BioSample |
SAMN09371524 |
| SRA |
SRX4169563 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3176679_ChIP-seq-delE1-delE3-L1-GR_rep1.ucsc.bedGraph.gz |
357.6 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
