|
| Status |
Public on Jul 28, 2023 |
| Title |
WT_MG_L1_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Mammary gland
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Mammary gland
strain: C57BL/6
developmental stage: Lactation day 1
genotype: wild-type
|
| Growth protocol |
Mouse mammary gland and liver tissues were harvested at day one of lactation.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
200ng of purified genomic DNA was used to create bisulfite sequencing libraries via the large DNA insert approach using the NEBNext® Enzymatic Methyl-seq Kit (New England Biolabs). In short, purified genomic DNA was fragmented, adenylated, and ligated to EM-seq adaptors. Bisulfite conversion was performed according to the manufacturer’s instructions. Internal unmethylated lambda DNA and CpG methylated pUC19 DNA controls were included with each library. Libraries were sequenced with a NovaSeq 6000 instrument (Illumina) to generate a minimum of 300 million paired-end 151 base reads per library.
Libraries for sequencing were prepared using standard New England Biolabs protocols.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw fastq files were quality trimmed using TrimGalore (version 0.6.7). Reads were aligned to the mouse genome (mm10) using Bismark71 (version 0.23.0). Mapped BAM files were sorted by query name, deduplicated using Picard (version 2.27.3) and finally sorted coordinates using Samtools (version 1.17). Integrative Genomics Viewer63 (version 2.3.98) was used for visualization.
Assembly: mm10
Supplementary files format and content: bismark.cov.bedGraph
|
| |
|
| 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 |
GPL24247 |
| Series (2) |
| GSE231438 |
Cell-specific and shared regulatory elements control a multi-gene locus active in mammary and salivary glands [Bisulfite-seq] |
| GSE231441 |
Cell-specific and shared regulatory elements control a multi-gene locus active in mammary and salivary glands |
|
| Relations |
| BioSample |
SAMN34507190 |
| SRA |
SRX20178048 |
