|
| Status |
Public on Aug 27, 2019 |
| Title |
Experiment A - 0.6 units AluI |
| Sample type |
SRA |
| |
|
| Source name |
Experiment A - 0.6 units AluI
|
| Organism |
Mus musculus |
| Characteristics |
strain: NIH/S
gender: Female
age: E13.5
tissue: liver
treatment: 0.6 units AluI
|
| Treatment protocol |
Nuclei were prepared from homogenised liver and digested with increasing amounts of the restriction enzyme AluI.
|
| Growth protocol |
Livers were dissected from female NIH/S mice (E13.5) and stored at -80C.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
AluI digestion was stopped and the DNA was sonicated.
Purified sonicated DNA was prepared for Illumina paired-end sequencing using New England Biolabs kit E7370. 50-nt paired reads were obtained using an Illumina NextSeq-500 machine.
New method: Quantitative DNA accessibility assay - "qDA-seq"
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
HepD-2_A3
|
| Data processing |
Sequences were aligned to the Mus musculus genome (mm10) using Bowtie2 with the parameters -X 5000 --very-sensitive
For every AluI motif (AGCT) found in the genome, we estimated the fraction of nuclei in which the given motif was cleaved by AluI, f_cut = N_cut=(N_cut + N_uncut), by counting the number of reads that were cut at this site (with an end at this site), N_cut, and the number of reads that were not cut at this site (overlapping the motif), N_uncut, using the Bioinformatics toolbox from Matlab.
Genome-wide profiles (bw files) containing the fraction of cut DNA at each site were generated using Matlab and wigToBigWig.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files containing the fraction of cut DNA at each AluI site along the mouse genome (for IGV genome browser)
|
| |
|
| Submission date |
Jun 12, 2018 |
| Last update date |
Aug 27, 2019 |
| Contact name |
Razvan V. Chereji |
| E-mail(s) |
razvan.chereji@nih.gov
|
| Phone |
301-435-8670
|
| Organization name |
National Institutes of Health
|
| Department |
NICHD
|
| Lab |
David J. Clark Lab
|
| Street address |
6 Center Drive, Room 2A14
|
| City |
Bethesda |
| State/province |
Maryland |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE115691 |
DNA accessibility is not the primary determinant of chromatin-mediated gene regulation (mouse) |
| GSE115693 |
DNA accessibility is not the primary determinant of chromatin-mediated gene regulation |
|
| Relations |
| BioSample |
SAMN09402746 |
| SRA |
SRX4199242 |
