|
| Status |
Public on Jul 07, 2020 |
| Title |
Male_Nudt7_Repl3_G169_M1 |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: Crl:CD1(ICR) (Charles River, strain code #022)
4c viewpoint: Nudt7 Enhancer
Sex: Male
age: 8 weeks
|
| Growth protocol |
Male and female CD1 mice, 8-9 weeks of age, were purchased from Charles River Laboratories (Crl:CD1(ICR)).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were isolated by ultracentrifugation in a high sucrose buffer then crosslinked with 0.8% formaldehyde for 9 minutes. 10M Crosslinked nuclei were processed as described previously (van de Werken et al 2012, Splinter et al 2012). DpnII was used as the primary restriction enzyme and Csp6I was used as the secondary. All ligations and disgestions were overnight (minimum 16 hr), and were verified by running a small aliquot in a 1% agarose gel.
Samples were amplified for 25 cycles of inverse PCR using a custom primer pair containing sequence specific to the indicated viewpoint as well as a partial adaptor sequence to facilitate barcoding in a secondary PCR reaction. To reduce the impact of PCR domination, samples represent pools of 6 independent (but otherwise identical) inverse PCR reactions. The reading primer was anchored directly at the DpnII cutsite, while the nonreading primer was positioned ~75bp from the Csp6I site. The samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 5 rounds of additional PCR per the manufacturer's instructions.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
4C-seq Library
|
| Data processing |
Library strategy: 4C-seq
READ FILTERING: The raw fastq file (with multiple viewpoints) was filtered to select only sequences that contain the known viewpoint-specific primers used.
READ MAPPING: Reads were aligned using Bowtie2 to a custom genome representing all uniquely-mappable DpnII cutsites in the mouse genome +/- the read length to keep only reads mapping to valid ligation junctions in the genome and increase mapping rate. To further improve mapping, unmapped reads were iteratively trimmed from the 3' end and mapping was attempted again.
NORMALIZATION: Reads were normalized to account for differences in sequencing depth (reads per million) and smoothed to represent the median normalized sequencing depth for a sliding window of 11 restriction fragments.
Genome_build: mm9
Supplementary_files_format_and_content: Supplemental bigWig tracks were generated representing a read depth normalized (reads per million) 4C signal for the merged male and female samples per viewpoint
|
| |
|
| Submission date |
May 08, 2019 |
| Last update date |
Jul 07, 2020 |
| Contact name |
David J. Waxman |
| E-mail(s) |
[email protected]
|
| Organization name |
Boston University
|
| Department |
Department of Biology and Bioinformatics Program
|
| Street address |
5 Cummington Mall
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE130911 |
4C-seq analysis of interactions with promoters and enhancers nearby five sex-specific genes, in male and female mouse liver |
| GSE131128 |
CTCF and Cohesin link sex-biased distal regulatory elements to sex-biased gene expression in mouse liver |
|
| Relations |
| BioSample |
SAMN11605274 |
| SRA |
SRX5807364 |
