|
| Status |
Public on Jul 28, 2023 |
| Title |
delCsn3-E2-SN_L1_NFIB_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary gland
strain: C57BL/6
developmental stage: Lactation day 1
genotype: delCsn3-E2-SN
antibody: STAT5A (Santa Cruz Biotechnology, sc-271542)
|
| Growth protocol |
Mouse mammary gland tissues were harvested at virgin, day six of pregnancy (p6) and day one of lactation (L1). Mouse salivary gland tissues were harvested from male mice of 2-month-old age.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
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: H3K27ac (Abcam, ab4729), RNA polymerase II (Abcam, ab5408), H3K4me1 (Active Motif, 39297) and H3K4me3 (Millipore, 07-473). Libraries for next-generation sequencing were prepared and sequenced with a HiSeq 3000 instrument (Illumina). Libraries for sequencing were prepared using standard Illumina protocols.
Libraries for sequencing were prepared using standard Illumina protocols.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
The fastq files were subjected to QC analyses using the FastQC tool (version 0.11.9). Quality filtering and alignment of the raw reads was done using Trimmomatic (version 0.36) and Bowtie (version 1.2.2) and Samtools (version 1.8), with the parameter ‘-m 1’ to keep only uniquely mapped reads, using the reference genome mm10. Homer30 (version 4.9.1) software was applied to generate bedGraph files, seperately. Integrative Genomics Viewer (version 2.3.98) was used for visualization with the parameter of -m 1 to retrieve only uniquely mapped reads, and Picard Tools to remove duplicates. Homer software was applied for the generation of bedGraph files.
Assembly: mm10
Supplementary files format and content: bedgraph of ChIP-seq
|
| |
|
| Submission date |
May 01, 2023 |
| Last update date |
Jul 28, 2023 |
| Contact name |
Hye Kyung Lee |
| E-mail(s) |
hyekyung.lee@nih.gov
|
| Phone |
301-435-6635
|
| Organization name |
National Institutes of Health (NIH)
|
| Department |
National Institute of Diabetes and Digestive and Kidney (NIDDK)
|
| Lab |
Laboratory of Genetics and Physiology
|
| Street address |
8 CENTER DR RM 107
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (2) |
| GSE231439 |
Cell-specific and shared regulatory elements control a multi-gene locus active in mammary and salivary glands [ChIP-Seq] |
| GSE231441 |
Cell-specific and shared regulatory elements control a multi-gene locus active in mammary and salivary glands |
|
| Relations |
| BioSample |
SAMN34507379 |
| SRA |
SRX20177936 |
